source: branches/3.18-stable/config/dist/raw-data-types.xml @ 7938

Last change on this file since 7938 was 6330, checked in by Nicklas Nordborg, 8 years ago

References #1751: Platform-specific files should not have svn:eol-style=native

Configuration files are now using LF as line endings.

  • Property svn:eol-style set to LF
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1<?xml version="1.0" encoding="UTF-8" ?>
2<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
3<!--
4  $Id: raw-data-types.xml 6330 2013-10-15 13:28:59Z nicklas $
5
6    Copyright (C) 2006 Nicklas Nordborg
7    Copyright (C) 2007 Johan Enell, Nicklas Nordborg
8
9    This file is part of BASE - BioArray Software Environment.
10    Available at http://base.thep.lu.se/
11
12    BASE is free software; you can redistribute it and/or modify it
13    under the terms of the GNU General Public License as published by
14    the Free Software Foundation; either version 3 of the License, or
15    (at your option) any later version.
16
17    BASE is distributed in the hope that it will be useful, but
18    WITHOUT ANY WARRANTY; without even the implied warranty of
19    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
20    General Public License for more details.
21
22    You should have received a copy of the GNU General Public License
23    along with BASE. If not, see <http://www.gnu.org/licenses/>.
24-->
25<raw-data-types>
26
27  <raw-data-type
28    id="genepix"
29    channels="2"
30    name="GenePix"
31    table="RawDataGenePix"
32    >
33    <property
34      name="diameter"
35      title="Spot diameter"
36      description="The diameter of the spot in µm"
37      column="diameter"
38      type="float"
39      averagemethod="none"
40    />
41    <property
42      name="ch1FgMedian"
43      title="Channel 1 foreground median"
44      description="The median of the foreground intensity in channel 1"
45      column="ch1_fg_median"
46      type="float"
47      channel="1"
48      averagemethod="arithmetic_mean"
49    />
50    <property
51      name="ch1FgMean"
52      title="Channel 1 foreground mean"
53      description="The mean of the foreground intensity in channel 1"
54      column="ch1_fg_mean"
55      type="float"
56      channel="1"
57      averagemethod="arithmetic_mean"
58    />
59    <property
60      name="ch1FgSd"
61      title="Channel 1 foreground standard deviation"
62      description="The standard deviation of the foreground intensity in channel 1"
63      column="ch1_fg_sd"
64      type="float"
65      channel="1"
66      averagemethod="arithmetic_mean"
67    />
68    <property
69      name="ch1BgMedian"
70      title="Channel 1 background median"
71      description="The median of the background intensity in channel 1"
72      column="ch1_bg_median"
73      type="float"
74      channel="1"
75      averagemethod="arithmetic_mean"
76    />
77    <property
78      name="ch1BgMean"
79      title="Channel 1 background mean"
80      description="The mean of the background intensity in channel 1"
81      column="ch1_bg_mean"
82      type="float"
83      channel="1"
84      averagemethod="arithmetic_mean"
85    />
86    <property
87      name="ch1BgSd"
88      title="Channel 1 background standard deviation"
89      description="The standard deviation of the background intensity in channel 1"
90      column="ch1_bg_sd"
91      type="float"
92      channel="1"
93      averagemethod="arithmetic_mean"
94    />
95    <property
96      name="ch1PercSd1"
97      title="% pixels &gt; 1 standard deviation above backgound"
98      description="Percentage of pixels more than 1 standard deviation
99        above the background intensity in channel 1"
100      column="ch1_perc_sd1"
101      type="int"
102      channel="1"
103      averagemethod="arithmetic_mean"
104    />
105    <property
106      name="ch1PercSd2"
107      title="% pixels &gt; 2 standard deviations above backgound"
108      description="Percentage of pixels more than 2 standard deviations
109        above the background intensity in channel 1"
110      column="ch1_perc_sd2"
111      type="int"
112      channel="1"
113      averagemethod="arithmetic_mean"
114    />
115    <property
116      name="ch1PercSat"
117      title="Percent saturated pixels"
118      description="Percentage of saturated pixels in channel 1"
119      column="ch1_perc_sat"
120      type="int"
121      channel="1"
122      averagemethod="arithmetic_mean"
123    />
124
125    <property
126      name="ch2FgMedian"
127      title="Channel 2 foreground median"
128      description="The median of the foreground intensity in channel 2"
129      column="ch2_fg_median"
130      type="float"
131      channel="2"
132      averagemethod="arithmetic_mean"
133    />
134    <property
135      name="ch2FgMean"
136      title="Channel 2 foreground mean"
137      description="The mean of the foreground intensity in channel 2"
138      column="ch2_fg_mean"
139      type="float"
140      channel="2"
141      averagemethod="arithmetic_mean"
142    />
143    <property
144      name="ch2FgSd"
145      title="Channel 2 foreground standard deviation"
146      description="The standard deviation of the foreground intensity in channel 2"
147      column="ch2_fg_sd"
148      type="float"
149      channel="2"
150      averagemethod="arithmetic_mean"
151    />
152    <property
153      name="ch2BgMedian"
154      title="Channel 2 background median"
155      description="The median of the background intensity in channel 2"
156      column="ch2_bg_median"
157      type="float"
158      channel="2"
159      averagemethod="arithmetic_mean"
160    />
161    <property
162      name="ch2BgMean"
163      title="Channel 2 background mean"
164      description="The mean of the background intensity in channel 2"
165      column="ch2_bg_mean"
166      type="float"
167      channel="2"
168      averagemethod="arithmetic_mean"
169    />
170    <property
171      name="ch2BgSd"
172      title="Channel 2 background standard deviation"
173      description="The standard deviation of the background intensity in channel 2"
174      column="ch2_bg_sd"
175      type="float"
176      channel="2"
177      averagemethod="arithmetic_mean"
178    />
179    <property
180      name="ch2PercSd1"
181      title="% pixels &gt; 1 standard deviation above backgound"
182      description="Percentage of pixels more than 1 standard deviation
183        above the background intensity in channel 2"
184      column="ch2_perc_sd1"
185      type="int"
186      channel="2"
187      averagemethod="arithmetic_mean"
188    />
189    <property
190      name="ch2PercSd2"
191      title="% pixels &gt; 2 standard deviations above backgound"
192      description="Percentage of pixels more than 2 standard deviations
193        above the background intensity in channel 2"
194      column="ch2_perc_sd2"
195      type="int"
196      channel="2"
197      averagemethod="arithmetic_mean"
198    />
199    <property
200      name="ch2PercSat"
201      title="Percent saturated pixels"
202      description="Percentage of saturated pixels in channel 2"
203      column="ch2_perc_sat"
204      type="int"
205      channel="2"
206      averagemethod="arithmetic_mean"
207    />
208
209    <property
210      name="ratiosSd"
211      title="Standard deviation of ratios"
212      description="The geometric standard deviation of the pixel intensity ratios."
213      column="ratios_sd"
214      type="float"
215      averagemethod="geometric_mean"
216    />
217    <property
218      name="rgnRatio"
219      title="Regression ratio"
220      description="The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature."
221      column="rgn_ratio"
222      type="float"
223      averagemethod="geometric_mean"
224    />
225    <property
226      name="rgnR2"
227      title="Rgn R2"
228      description="The coefficient of determination for the current regression value."
229      column="rgn_r2"
230      type="float"
231      averagemethod="geometric_mean"
232    />
233
234    <property
235      name="fgPixels"
236      title="Foreground pixels"
237      description="Number of foreground pixels"
238      column="fg_pixels"
239      type="int"
240      averagemethod="arithmetic_mean"
241    />
242    <property
243      name="bgPixels"
244      title="Background pixels"
245      description="Number of background pixels"
246      column="bg_pixels"
247      type="int"
248      averagemethod="arithmetic_mean"
249    />
250    <property
251      name="flags"
252      title="Flags"
253      description="Flags"
254      column="flags"
255      type="int"
256      averagemethod="none"
257    />
258    <property
259      name="mValue"
260      title="M value"
261      description="M value"
262      column="m_value"
263      type="float"
264      averagemethod="arithmetic_mean"
265    />
266    <property
267      name="CV"
268      title="CV"
269      description="CV"
270      column="cv"
271      type="float"
272      averagemethod="none"
273    />
274    <intensity-formula
275      name="mean"
276      title="Mean FG - Mean BG"
277      description="Subtract mean background from mean foreground"
278      >
279      <formula 
280        channel="1"
281        expression="raw('ch1FgMean') - raw('ch1BgMean')"
282      />
283      <formula 
284        channel="2"
285        expression="raw('ch2FgMean') - raw('ch2BgMean')"
286      />
287    </intensity-formula>
288    <intensity-formula
289      name="median"
290      title="Median FG - Median BG"
291      description="Subtract meadian background from median foreground"
292      >
293      <formula 
294        channel="1"
295        expression="raw('ch1FgMedian') - raw('ch1BgMedian')"
296      />
297      <formula 
298        channel="2"
299        expression="raw('ch2FgMedian') - raw('ch2BgMedian')"
300      />
301    </intensity-formula>
302    <intensity-formula
303      name="medianmean"
304      title="Median FG - Mean BG"
305      description="Subtract mean background from median foreground"
306      >
307      <formula 
308        channel="1"
309        expression="raw('ch1FgMedian') - raw('ch1BgMean')"
310      />
311      <formula 
312        channel="2"
313        expression="raw('ch2FgMedian') - raw('ch2BgMean')"
314      />
315    </intensity-formula>
316    <intensity-formula
317      name="meanmedian"
318      title="Mean FG - Median BG"
319      description="Subtract median background from mean foreground"
320      >
321      <formula 
322        channel="1"
323        expression="raw('ch1FgMean') - raw('ch1BgMedian')"
324      />
325      <formula 
326        channel="2"
327        expression="raw('ch2FgMean') - raw('ch2BgMedian')"
328      />
329    </intensity-formula>
330    <intensity-formula
331      name="meanfg"
332      title="Mean FG"
333      description="Mean foreground"
334      >
335      <formula 
336        channel="1"
337        expression="raw('ch1FgMean')"
338      />
339      <formula 
340        channel="2"
341        expression="raw('ch2FgMean')"
342      />
343    </intensity-formula>
344    <intensity-formula
345      name="medianfg"
346      title="Median FG"
347      description="Median foreground"
348      >
349      <formula 
350        channel="1"
351        expression="raw('ch1FgMedian')"
352      />
353      <formula 
354        channel="2"
355        expression="raw('ch2FgMedian')"
356      />
357    </intensity-formula>
358    <intensity-formula
359      name="medianfgmeanmedianbg"
360      title="Median FG - Mean(Median BG)"
361      description="Subtract mean of median backgrounds from median foreground"
362      >
363      <formula 
364        channel="1"
365        expression="raw('ch1FgMedian') - mean('ch1BgMedian')"
366      />
367      <formula 
368        channel="2"
369        expression="raw('ch2FgMedian') - mean('ch2BgMedian')"
370      />
371    </intensity-formula>
372    <intensity-formula
373      name="meanfgmeanmeanbg"
374      title="Mean FG - Mean(Mean BG)"
375      description="Subtract mean of mean backgrounds from mean foreground"
376      >
377      <formula 
378        channel="1"
379        expression="raw('ch1FgMean') - mean('ch1BgMean')"
380      />
381      <formula 
382        channel="2"
383        expression="raw('ch2FgMean') - mean('ch2BgMean')"
384      />
385    </intensity-formula>
386    <intensity-formula
387      name="medianfgmeanmeanbg"
388      title="Median FG - Mean(Mean BG)"
389      description="Subtract mean of mean backgrounds from median foreground"
390      >
391      <formula 
392        channel="1"
393        expression="raw('ch1FgMedian') - mean('ch1BgMean')"
394      />
395      <formula 
396        channel="2"
397        expression="raw('ch2FgMedian') - mean('ch2BgMean')"
398      />
399    </intensity-formula>
400    <intensity-formula
401      name="meanfgmeanmedianbg"
402      title="Mean FG - Mean(Median BG)"
403      description="Subtract mean of median backgrounds from mean foreground"
404      >
405      <formula 
406        channel="1"
407        expression="raw('ch1FgMean') - mean('ch1BgMedian')"
408      />
409      <formula 
410        channel="2"
411        expression="raw('ch2FgMean') - mean('ch2BgMedian')"
412      />
413    </intensity-formula>
414  </raw-data-type>
415 
416  <raw-data-type
417    id="bzscan"
418    channels="1"
419    name="BZScan"
420    table="RawDataBZScan"
421    >
422    <property
423      name="QImageConst"
424      title="Q(image,const)"
425      description="Spot intensity based on user-provided diameter and measured data."
426      column="q_image_const"
427      type="float"
428    />
429    <property
430      name="QImageVar"
431      title="Q(image,var)"
432      description="Spot intensity based on computed diameter and measured data."
433      column="q_image_var"
434      type="float"
435    />
436    <property
437      name="QFitConst"
438      title="Q(fit,const)"
439      description="Spot intensity based on user-provided diameter and theoretical fit to the data."
440      column="q_fit_const"
441      type="float"
442    />
443    <property
444      name="QFitVar"
445      title="Q(fit,var)"
446      description="Spot intensity based on computed diameter and and theoretical fit to the data."
447      column="q_fit_var"
448      type="float"
449    />
450    <property
451      name="FitCorrection"
452      title="Fit correction"
453      description="Background level by unit surface."
454      column="fit_correction"
455      type="float"
456    />
457    <property
458      name="QM"
459      title="Quality metric"
460      description="Quality metric: distance between measured data and theoretical fit."
461      column="quality_metric"
462      type="float"
463    />
464    <property
465      name="SpotQuality"
466      title="Spot quality"
467      description="Present/Absent (automatic guess)."
468      column="spot_quality"
469      type="boolean"
470    />
471    <property
472      name="OvershiningCorrection"
473      title="Overshining correction"
474      description="Correction for overshining by unit radius."
475      column="overshining"
476      type="float"
477    />
478    <intensity-formula
479      name="QImageConst"
480      title="Q(image,const)"
481      description="Spot intensity based on user-provided diameter and measured data"
482      >
483      <formula 
484        channel="1"
485        expression="raw('QImageConst')"
486      />
487    </intensity-formula>
488    <intensity-formula
489      name="QImageVar"
490      title="Q(image,var)"
491      description="Spot intensity based on computed diameter and measured data"
492      >
493      <formula 
494        channel="1"
495        expression="raw('QImageVar')"
496      />
497    </intensity-formula>
498    <intensity-formula
499      name="QFitConst"
500      title="Q(fit,const)"
501      description="Spot intensity based on user-provided diameter and theoretical fit to the data"
502      >
503      <formula 
504        channel="1"
505        expression="raw('QFitConst')"
506      />
507    </intensity-formula>
508    <intensity-formula
509      name="QFitVar"
510      title="Q(fit,var)"
511      description="Spot intensity based on computed diameter and and theoretical fit to the data"
512      >
513      <formula 
514        channel="1"
515        expression="raw('QFitVar')"
516      />
517    </intensity-formula>
518  </raw-data-type>
519 
520  <raw-data-type
521    id="aida"
522    channels="2"
523    name="AIDA"
524    table="RawDataAida"
525    >
526    <property
527      name="area"
528      title="Area"
529      description="Spot area in pixels."
530      column="area"
531      type="float"
532      averagemethod="arithmetic_mean"
533    />
534    <property
535      name="ch1Integral"
536      title="Channel 1 integral"
537      description="Integrated raw intensity of spot channel 1."
538      column="ch1_integral"
539      type="float"
540      channel="1"
541      averagemethod="arithmetic_mean"
542    />
543    <property
544      name="ch1Mean"
545      title="Channel 1 mean"
546      description="Mean (Integral/Area) channel 1."
547      column="ch1_mean"
548      type="float"
549      channel="1"
550      averagemethod="arithmetic_mean"
551    />
552    <property
553      name="ch1Median"
554      title="Channel 1 median"
555      description="Median of the raw pixel intensity of spot channel 1."
556      column="ch1_median"
557      type="float"
558      channel="1"
559      averagemethod="arithmetic_mean"
560    />
561    <property
562      name="ch1Bkg"
563      title="Channel 1 background"
564      description="Standard deviation of background channel 1."
565      column="ch1_bkg"
566      type="float"
567      channel="1"
568      averagemethod="arithmetic_mean"
569    />
570    <property
571      name="ch1Sat"
572      title="Channel 1 saturated"
573      description="Measure of saturation pixels channel 1."
574      column="ch1_sat"
575      type="float"
576      channel="1"
577      averagemethod="arithmetic_mean"
578    />
579    <property
580      name="ch1Hom"
581      title="Channel 1 homogenity"
582      description="Percentage of dot deviation from homogenous intensity distribution channel 1."
583      column="ch1_hom"
584      type="float"
585      channel="1"
586      averagemethod="arithmetic_mean"
587    />
588    <property
589      name="ch1Quality"
590      title="Channel 1 quality"
591      description="Quality flag channel 1."
592      column="ch1_quality"
593      type="boolean"
594      channel="1"
595      averagemethod="none"
596    />
597    <property
598      name="ch2Integral"
599      title="Channel 2 integral"
600      description="Integrated raw intensity of spot channel 2."
601      column="ch2_integral"
602      type="float"
603      channel="2"
604      averagemethod="arithmetic_mean"
605    />
606    <property
607      name="ch2Mean"
608      title="Channel 2 mean"
609      description="Mean (Integral/Area) channel 2."
610      column="ch2_mean"
611      type="float"
612      channel="2"
613      averagemethod="arithmetic_mean"
614    />
615    <property
616      name="ch2Median"
617      title="Channel 2 median"
618      description="Median of the raw pixel intensity of spot channel 2."
619      column="ch2_median"
620      type="float"
621      channel="2"
622      averagemethod="arithmetic_mean"
623    />
624    <property
625      name="ch2Bkg"
626      title="Channel 2 background"
627      description="Standard deviation of background channel 2."
628      column="ch2_bkg"
629      type="float"
630      channel="2"
631      averagemethod="arithmetic_mean"
632    />
633    <property
634      name="ch2Sat"
635      title="Channel 2 saturated"
636      description="Measure of saturation pixels channel 2."
637      column="ch2_sat"
638      type="float"
639      channel="2"
640      averagemethod="arithmetic_mean"
641    />
642    <property
643      name="ch2Hom"
644      title="Channel 2 homogenity"
645      description="Percentage of dot deviation from homogenous intensity distribution channel 2."
646      column="ch2_hom"
647      type="float"
648      channel="2"
649      averagemethod="arithmetic_mean"
650    />
651    <property
652      name="ch2Quality"
653      title="Channel 2 quality"
654      description="Quality flag channel 2."
655      column="ch2_quality"
656      type="boolean"
657      channel="2"
658      averagemethod="none"
659    />
660    <intensity-formula
661      name="mean"
662      title="Mean"
663      description="Mean of the raw pixel intensity (Integral/Area)"
664      >
665      <formula 
666        channel="1"
667        expression="raw('ch1Mean')"
668      />
669      <formula 
670        channel="2"
671        expression="raw('ch2Mean')"
672      />
673    </intensity-formula>
674    <intensity-formula
675      name="median"
676      title="Median"
677      description="Median of the raw pixel intensity"
678      >
679      <formula 
680        channel="1"
681        expression="raw('ch1Median')"
682      />
683      <formula 
684        channel="2"
685        expression="raw('ch2Median')"
686      />
687    </intensity-formula>
688  </raw-data-type>
689
690  <raw-data-type
691    id="agilent"
692    channels="2"
693    name="Agilent"
694    table="RawDataAgilent"
695    >
696    <property
697      name="LogRatio"
698      title="Log ratio"
699      description="log(REDsignal/GREENsignal) per feature. Signals in both channels are post dye normalization. If SURROGATES are disabled, then this value will be set to: -2 if DyeNormRedSig &lt;= 0.0 amp; DyeNormGreenSig &gt; 0.0; 2 if DyeNormRedSig &gt; 0.0 &amp; DyeNormGreenSig &lt;= 0.0; and 0 if DyeNormRedSig &lt;= 0.0 amp; DyeNormGreenSig &lt;= 0.0."
700      column="log_ratio"
701      type="float"
702      averagemethod="arithmetic_mean"
703    />
704    <property
705      name="PValueLogRatio"
706      title="P value log ratio"
707      description="Significance level of the Log Ratio computed for a feature."
708      column="pvalue_log_ratio"
709      type="float"
710      averagemethod="arithmetic_mean"
711    />
712    <property
713      name="gSurrogateUsed"
714      title="G surrogate used"
715      description="The green surrogate value used."
716      column="g_surrogate_used"
717      channel="1"
718      type="float"
719      averagemethod="none"
720    />
721    <property
722      name="rSurrogateUsed"
723      title="R surrogate used"
724      description="The red surrogate value used."
725      column="r_surrogate_used"
726      channel="2"
727      type="float"
728      averagemethod="none"
729    />
730    <property
731      name="gIsFound"
732      title="G is found"
733      description="A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong."
734      column="g_is_found"
735      channel="1"
736      type="boolean"
737      averagemethod="none"
738    />
739    <property
740      name="rIsFound"
741      title="R is found"
742      description="A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong."
743      column="r_is_found"
744      channel="2"
745      type="boolean"
746      averagemethod="none"
747    />
748    <property
749      name="gProcessedSignal"
750      title="G processed signal"
751      description="The propagated feature signal, per channel, used for computation of log ratio."
752      column="g_processed_signal"
753      channel="1"
754      type="float"
755      averagemethod="arithmetic_mean"
756    />
757    <property
758      name="rProcessedSignal"
759      title="R processed signal"
760      description="The propagated feature signal, per channel, used for computation of log ratio."
761      column="r_processed_signal"
762      channel="2"
763      type="float"
764      averagemethod="arithmetic_mean"
765    />
766    <property
767      name="gNumPixOLHi"
768      title="G high outlier pixels"
769      description="Number of outlier pixels per feature with intensity &gt; upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations."
770      column="g_high_outlier_pixels"
771      channel="1"
772      type="int"
773      averagemethod="arithmetic_mean"
774    />
775    <property
776      name="rNumPixOLHi"
777      title="R high outlier pixels"
778      description="Number of outlier pixels per feature with intensity &gt; upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations."
779      column="r_high_outlier_pixels"
780      channel="2"
781      type="int"
782      averagemethod="arithmetic_mean"
783    />
784    <property
785      name="gNumPixOLLo"
786      title="G low outlier pixels"
787      description="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."
788      column="g_low_outlier_pixels"
789      channel="1"
790      type="int"
791      averagemethod="arithmetic_mean"
792    />
793    <property
794      name="rNumPixOLLo"
795      title="R low outlier pixels"
796      description="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."
797      column="r_low_outlier_pixels"
798      channel="2"
799      type="int"
800      averagemethod="arithmetic_mean"
801    />
802    <property
803      name="gNumPix"
804      title="G pixels"
805      description="Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels."
806      column="g_pixels"
807      channel="1"
808      type="int"
809      averagemethod="arithmetic_mean"
810    />
811    <property
812      name="rNumPix"
813      title="R pixels"
814      description="Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels."
815      column="r_pixels"
816      channel="2"
817      type="int"
818      averagemethod="arithmetic_mean"
819    />
820    <property
821      name="gMeanSignal"
822      title="G mean signal"
823      description="Raw mean signal of feature in green channel."
824      column="g_mean_signal"
825      channel="1"
826      type="float"
827      averagemethod="arithmetic_mean"
828    />
829    <property
830      name="rMeanSignal"
831      title="R mean signal"
832      description="Raw mean signal of feature in red channel."
833      column="r_mean_signal"
834      channel="2"
835      type="float"
836      averagemethod="arithmetic_mean"
837    />
838    <property
839      name="gMedianSignal"
840      title="G median signal"
841      description="Raw median signal of feature in green channel."
842      column="g_median_signal"
843      channel="1"
844      type="float"
845      averagemethod="arithmetic_mean"
846    />
847    <property
848      name="rMedianSignal"
849      title="R median signal"
850      description="Raw median signal of feature in red channel."
851      column="r_median_signal"
852      channel="2"
853      type="float"
854      averagemethod="arithmetic_mean"
855    />
856    <property
857      name="gBGNumPix"
858      title="G background pixels"
859      description="Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel."
860      column="g_bg_pixels"
861      channel="1"
862      type="int"
863      averagemethod="arithmetic_mean"
864    />
865    <property
866      name="rBGNumPix"
867      title="R background pixels"
868      description="Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel."
869      column="r_bg_pixels"
870      channel="2"
871      type="int"
872      averagemethod="arithmetic_mean"
873    />
874    <property
875      name="gBGMeanSignal"
876      title="G mean background"
877      description="Mean local background signal (local to corresponding feature) computed per channel."
878      column="g_bg_mean_signal"
879      channel="1"
880      type="float"
881      averagemethod="arithmetic_mean"
882    />
883    <property
884      name="rBGMeanSignal"
885      title="R mean background"
886      description="Mean local background signal (local to corresponding feature) computed per channel."
887      column="r_bg_mean_signal"
888      channel="2"
889      type="float"
890      averagemethod="arithmetic_mean"
891    />
892    <property
893      name="gBGMedianSignal"
894      title="G median background"
895      description="Median local background signal (local to corresponding feature) computed per channel."
896      column="g_bg_median_signal"
897      channel="1"
898      type="float"
899      averagemethod="arithmetic_mean"
900    />
901    <property
902      name="rBGMedianSignal"
903      title="R median background"
904      description="Median local background signal (local to corresponding feature) computed per channel."
905      column="r_bg_median_signal"
906      channel="2"
907      type="float"
908      averagemethod="arithmetic_mean"
909    />
910    <property
911      name="gNumSatPix"
912      title="G saturated pixels"
913      description="Total number of saturated pixels per feature, computed per channel."
914      column="g_sat_pixels"
915      channel="1"
916      type="int"
917      averagemethod="arithmetic_mean"
918    />
919    <property
920      name="rNumSatPix"
921      title="R saturated pixels"
922      description="Total number of saturated pixels per feature, computed per channel."
923      column="r_sat_pixels"
924      channel="2"
925      type="int"
926      averagemethod="arithmetic_mean"
927    />
928    <property
929      name="gIsSaturated"
930      title="G is saturated"
931      description="Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated."
932      column="g_is_saturated"
933      channel="1"
934      type="boolean"
935      averagemethod="none"
936    />
937    <property
938      name="rIsSaturated"
939      title="R is saturated"
940      description="Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated."
941      column="r_is_saturated"
942      channel="2"
943      type="boolean"
944      averagemethod="none"
945    />
946    <property
947      name="PixCorrelation"
948      title="Pix correlation"
949      description="Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co-vary."
950      column="pix_correlation"
951      type="float"
952      averagemethod="geometric_mean"
953    />
954    <property
955      name="BGPixCorrelation"
956      title="BG pix correlation"
957      description="Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co-vary."
958      column="bg_pix_correlation"
959      type="float"
960      averagemethod="geometric_mean"
961    />
962    <property
963      name="gIsFeatNonUnifOL"
964      title="G non-uniform outlier"
965      description="Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
966      column="g_nonuniform_outlier"
967      channel="1"
968      type="boolean"
969      averagemethod="none"
970    />
971    <property
972      name="rIsFeatNonUnifOL"
973      title="R non-uniform outlier"
974      description="Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
975      column="r_nonuniform_outlier"
976      channel="2"
977      type="boolean"
978    />
979    <property
980      name="gIsBGNonUnifOL"
981      title="G bg non-uniform outlier"
982      description="Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
983      column="g_bg_nonuniform_outlier"
984      channel="1"
985      type="boolean"
986    />
987    <property
988      name="rIsBGNonUnifOL"
989      title="R bg non-uniform outlier"
990      description="Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
991      column="r_bg_nonuniform_outlier"
992      channel="2"
993      type="boolean"
994    />
995    <property
996      name="gIsFeatPopnOL"
997      title="G population outlier"
998      description="Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier."
999      column="g_population_outlier"
1000      channel="1"
1001      type="boolean"
1002    />
1003    <property
1004      name="rIsFeatPopnOL"
1005      title="R population outlier"
1006      description="Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier."
1007      column="r_population_outlier"
1008      channel="2"
1009      type="boolean"
1010      averagemethod="none"
1011    />
1012    <property
1013      name="gIsBGPopnOL"
1014      title="G bg population outlier"
1015      description="Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier."
1016      column="g_bg_population_outlier"
1017      channel="1"
1018      type="boolean"
1019      averagemethod="none"
1020    />
1021    <property
1022      name="rIsBGPopnOL"
1023      title="R bg population outlier"
1024      description="Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier."
1025      column="r_bg_population_outlier"
1026      channel="2"
1027      type="boolean"
1028      averagemethod="none"
1029    />
1030    <property
1031      name="IsManualFlag"
1032      title="Manual flag"
1033      description="If a feature has been moved manually this flag will be set to 1."
1034      column="manual_flag"
1035      type="boolean"
1036      averagemethod="none"
1037    />
1038    <property
1039      name="gBGSubSignal"
1040      title="G net signal"
1041      description="The net green signal following the subtraction of the background from the raw mean green signal."
1042      column="g_net_signal"
1043      channel="1"
1044      type="float"
1045    />
1046    <property
1047      name="rBGSubSignal"
1048      title="R net signal"
1049      description="The net red signal following the subtraction of the background from the raw mean red signal."
1050      column="r_net_signal"
1051      channel="2"
1052      type="float"
1053      averagemethod="arithmetic_mean"
1054    />
1055    <property
1056      name="BGSubSigCorrelation"
1057      title="BG correlation"
1058      description="Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space."
1059      column="bg_correlation"
1060      type="float"
1061      averagemethod="geometric_mean"
1062    />
1063    <property
1064      name="gIsPosAndSignif"
1065      title="G > 0 and significant"
1066      description="Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background."
1067      column="g_significant"
1068      channel="1"
1069      type="boolean"
1070      averagemethod="none"
1071    />
1072    <property
1073      name="rIsPosAndSignif"
1074      title="R > 0 and significant"
1075      description="Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background."
1076      column="r_significant"
1077      channel="2"
1078      type="boolean"
1079      averagemethod="none"
1080    />
1081    <property
1082      name="gPValFeatEqBG"
1083      title="G p-value"
1084      description="P-value from t-test of significance between green Mean signal and green background."
1085      column="g_pvalue"
1086      channel="1"
1087      type="float"
1088      averagemethod="none"
1089    />
1090    <property
1091      name="rPValFeatEqBG"
1092      title="R p-value"
1093      description="P-value from t-test of significance between red Mean signal and red background."
1094      column="r_pvalue"
1095      channel="2"
1096      type="float"
1097      averagemethod="none"
1098    />
1099    <property
1100      name="gNumBGUsed"
1101      title="G background pixels"
1102      description="A count of the number of background pixels used in the green channel."
1103      column="g_numbg_used"
1104      channel="1"
1105      type="int"
1106      averagemethod="arithmetic_mean"
1107    />
1108    <property
1109      name="rNumBGUsed"
1110      title="R background pixels"
1111      description="A count of the number of background pixels used in the red channel."
1112      column="r_numbg_used"
1113      channel="2"
1114      type="int"
1115      averagemethod="arithmetic_mean"
1116    />
1117    <property
1118      name="gIsWellAboveBG"
1119      title="G well above bg"
1120      description="Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG."
1121      column="g_above_bg"
1122      channel="1"
1123      type="boolean"
1124      averagemethod="none"
1125    />
1126    <property
1127      name="rIsWellAboveBG"
1128      title="R well above bg"
1129      description="Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG."
1130      column="r_above_bg"
1131      channel="2"
1132      type="boolean"
1133      averagemethod="none"
1134    />
1135    <property
1136      name="gBGUsed"
1137      title="G bg used"
1138      description="Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel."
1139      column="g_bg_used"
1140      channel="1"
1141      type="float"
1142      averagemethod="arithmetic_mean"
1143    />
1144    <property
1145      name="rBGUsed"
1146      title="R bg used"
1147      description="Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel."
1148      column="r_bg_used"
1149      channel="2"
1150      type="float"
1151      averagemethod="arithmetic_mean"
1152    />
1153    <property
1154      name="IsNormalization"
1155      title="Normalization"
1156      description="A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used."
1157      column="is_normalization"
1158      type="boolean"
1159      averagemethod="none"
1160    />
1161    <property
1162      name="gDyeNormSignal"
1163      title="G normalized signal"
1164      description="The dye normalized signal in the green channel."
1165      column="g_normalized"
1166      channel="1"
1167      type="float"
1168      averagemethod="arithmetic_mean"
1169    />
1170    <property
1171      name="rDyeNormSignal"
1172      title="R normalized signal"
1173      description="The dye normalized signal in the green channel."
1174      column="r_normalized"
1175      channel="2"
1176      type="float"
1177      averagemethod="arithmetic_mean"
1178    />
1179    <property
1180      name="DyeNormCorrelation"
1181      title="Normalized correlation"
1182      description="Dye normalized red and green pixel correlation."
1183      column="norm_correlation"
1184      type="float"
1185      averagemethod="none"
1186    />
1187    <property
1188      name="ErrorModel"
1189      title="Error model"
1190      description="ErrorModel Indicates the error model that the user chose for feature extraction. A 0 indicates use of the Propogated Error Model. A 1 indicates use of the Universal Error Model."
1191      column="error_model"
1192      type="int"
1193      averagemethod="none"
1194    />
1195    <property
1196      name="xDev"
1197      title="X dev"
1198      description="Used to compute the Log Ratio PValue."
1199      column="x_dev"
1200      type="float"
1201      averagemethod="none"
1202    />
1203    <property
1204      name="gSpatialDetrendIsInFilteredSet"
1205      title="G spatial trend"
1206      description="Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features."
1207      column="g_spatial_trend"
1208      channel="1"
1209      type="boolean"
1210      averagemethod="none"
1211    />
1212    <property
1213      name="rSpatialDetrendIsInFilteredSet"
1214      title="R spatial trend"
1215      description="Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features."
1216      column="r_spatial_trend"
1217      channel="2"
1218      type="boolean"
1219      averagemethod="none"
1220    />
1221    <property
1222      name="gSpatialDetrendSurfaceValue"
1223      title="G surface value"
1224      description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1225      column="g_surface_value"
1226      channel="1"
1227      type="float"
1228      averagemethod="arithmetic_mean"
1229    />
1230    <property
1231      name="rSpatialDetrendSurfaceValue"
1232      title="R surface value"
1233      description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1234      column="r_surface_value"
1235      channel="2"
1236      type="float"
1237      averagemethod="arithmetic_mean"
1238    />
1239    <intensity-formula
1240      name="mean"
1241      title="Mean FG - Mean BG"
1242      description="Subtract mean background from mean foreground"
1243      >
1244      <formula 
1245        channel="1"
1246        expression="raw('gMeanSignal') - raw('gBGMeanSignal')"
1247      />
1248      <formula 
1249        channel="2"
1250        expression="raw('rMeanSignal') - raw('rBGMeanSignal')"
1251      />
1252    </intensity-formula>
1253    <intensity-formula
1254      name="median"
1255      title="Median FG - Median BG"
1256      description="Subtract meadian background from median foreground"
1257      >
1258      <formula 
1259        channel="1"
1260        expression="raw('gMedianSignal') - raw('gBGMedianSignal')"
1261      />
1262      <formula 
1263        channel="2"
1264        expression="raw('rMedianSignal') - raw('rBGMedianSignal')"
1265      />
1266    </intensity-formula>
1267    <intensity-formula
1268      name="medianmean"
1269      title="Median FG - Mean BG"
1270      description="Subtract mean background from median foreground"
1271      >
1272      <formula 
1273        channel="1"
1274        expression="raw('gMedianSignal') - raw('gBGMeanSignal')"
1275      />
1276      <formula 
1277        channel="2"
1278        expression="raw('rMedianSignal') - raw('rBGMeanSignal')"
1279      />
1280    </intensity-formula>
1281    <intensity-formula
1282      name="meanmedian"
1283      title="Mean FG - Median BG"
1284      description="Subtract median background from mean foreground"
1285      >
1286      <formula 
1287        channel="1"
1288        expression="raw('gMeanSignal') - raw('gBGMedianSignal')"
1289      />
1290      <formula 
1291        channel="2"
1292        expression="raw('rMeanSignal') - raw('rBGMedianSignal')"
1293      />
1294    </intensity-formula>
1295    <intensity-formula
1296      name="meanfg"
1297      title="Mean FG"
1298      description="Mean foreground"
1299      >
1300      <formula 
1301        channel="1"
1302        expression="raw('gMeanSignal')"
1303      />
1304      <formula 
1305        channel="2"
1306        expression="raw('rMeanSignal')"
1307      />
1308    </intensity-formula>
1309    <intensity-formula
1310      name="medianfg"
1311      title="Median FG"
1312      description="Median foreground"
1313      >
1314      <formula 
1315        channel="1"
1316        expression="raw('gMedianSignal')"
1317      />
1318      <formula 
1319        channel="2"
1320        expression="raw('rMedianSignal')"
1321      />
1322    </intensity-formula>
1323    <intensity-formula
1324      name="medianfgmeanmedianbg"
1325      title="Median FG - Mean(Median BG)"
1326      description="Subtract mean of median backgrounds from median foreground"
1327      >
1328      <formula 
1329        channel="1"
1330        expression="raw('gMedianSignal') - mean('gBGMedianSignal')"
1331      />
1332      <formula 
1333        channel="2"
1334        expression="raw('rMedianSignal') - mean('rBGMedianSignal')"
1335      />
1336    </intensity-formula>
1337    <intensity-formula
1338      name="meanfgmeanmeanbg"
1339      title="Mean FG - Mean(Mean BG)"
1340      description="Subtract mean of mean backgrounds from mean foreground"
1341      >
1342      <formula 
1343        channel="1"
1344        expression="raw('gMeanSignal') - mean('gBGMeanSignal')"
1345      />
1346      <formula 
1347        channel="2"
1348        expression="raw('rMeanSignal') - mean('rBGMeanSignal')"
1349      />
1350    </intensity-formula>
1351    <intensity-formula
1352      name="medianfgmeanmeanbg"
1353      title="Median FG - Mean(Mean BG)"
1354      description="Subtract mean of mean backgrounds from median foreground"
1355      >
1356      <formula 
1357        channel="1"
1358        expression="raw('gMedianSignal') - mean('gBGMeanSignal')"
1359      />
1360      <formula 
1361        channel="2"
1362        expression="raw('rMedianSignal') - mean('rBGMeanSignal')"
1363      />
1364    </intensity-formula>
1365    <intensity-formula
1366      name="meanfgmeanmedianbg"
1367      title="Mean FG - Mean(Median BG)"
1368      description="Subtract mean of median backgrounds from mean foreground"
1369      >
1370      <formula 
1371        channel="1"
1372        expression="raw('gMeanSignal') - mean('gBGMedianSignal')"
1373      />
1374      <formula 
1375        channel="2"
1376        expression="raw('rMeanSignal') - mean('rBGMedianSignal')"
1377      />
1378    </intensity-formula>
1379  </raw-data-type>
1380 
1381  <raw-data-type
1382    id="chipskipper"
1383    channels="2"
1384    name="ChipSkipper"
1385    table="RawDataChipSkipper"
1386    >
1387    <property
1388      name="Line_Counter"
1389      title="Line counter"
1390      description="Line counter."
1391      column="line_counter"
1392      type="int"
1393      averagemethod="none"
1394    />
1395    <property
1396      name="Flags"
1397      title="Flags"
1398      description="Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad."
1399      column="flags"
1400      type="string"
1401      averagemethod="none"
1402    />
1403    <property
1404      name="GS_Flags"
1405      title="GS flags"
1406      description="P = pass or M = marginal flag."
1407      column="gs_flags"
1408      type="string"
1409      averagemethod="none"
1410    />
1411    <property
1412      name="Cy3_Volume"
1413      title="Cy3 volume"
1414      description="Total integrated signal intensity in color channel Cy3."
1415      column="cy3_volume"
1416      channel="1"
1417      type="int"
1418      averagemethod="arithmetic_mean"
1419    />
1420    <property
1421      name="Cy3_AvVolpixel"
1422      title="Cy3 average intensity"
1423      description="Average intensity per pixel in color channel Cy3."
1424      column="cy3_avg"
1425      channel="1"
1426      type="float"
1427      averagemethod="arithmetic_mean"
1428    />
1429    <property
1430      name="Cy3_BGArith"
1431      title="Cy3 background (arithmetic)"
1432      description="Arithmetic average for local background in color channel Cy3."
1433      column="cy3_bg_arith"
1434      channel="1"
1435      type="float"
1436      averagemethod="arithmetic_mean"
1437    />
1438    <property
1439      name="Cy3_BGGeom"
1440      title="Cy3 background (geometric)"
1441      description="Geometric average for local background in color channel Cy3."
1442      column="cy3_bg_geom"
1443      channel="1"
1444      type="float"
1445      averagemethod="geometric_mean"
1446    />
1447    <property
1448      name="Cy3_BGMedian"
1449      title="Cy3 background (median)"
1450      description="Median average for local background in color channel Cy3."
1451      column="cy3_bg_median"
1452      channel="1"
1453      type="float"
1454      averagemethod="arithmetic_mean"
1455    />
1456    <property
1457      name="Cy3_BG_Tot"
1458      title="Cy3 background (total)"
1459      description="Total integrated background in color channel Cy3."
1460      column="cy3_bg_total"
1461      channel="1"
1462      type="float"
1463      averagemethod="arithmetic_mean"
1464    />
1465    <property
1466      name="Cy3_VolBG"
1467      title="Cy3 reduced intensity"
1468      description="Background reduced intensity of colour channel Cy3."
1469      column="cy3_reduced"
1470      channel="1"
1471      type="float"
1472      averagemethod="arithmetic_mean"
1473    />
1474    <property
1475      name="Cy3_Spotarea"
1476      title="Cy3 spot area"
1477      description="Area of spot in colour channel Cy3 in pixels."
1478      column="cy3_area"
1479      channel="1"
1480      type="float"
1481      averagemethod="arithmetic_mean"
1482    />
1483    <property
1484      name="Cy3_Satpixel"
1485      title="Cy3 saturated pixels"
1486      description="Number of saturated pixel in color channel Cy3."
1487      column="cy3_saturated"
1488      channel="1"
1489      type="float"
1490      averagemethod="arithmetic_mean"
1491    />
1492    <property
1493      name="Cy5_Volume"
1494      title="Cy5 volume"
1495      description="Total integrated signal intensity in color channel Cy5."
1496      column="cy5_volume"
1497      channel="2"
1498      type="int"
1499      averagemethod="arithmetic_mean"
1500    />
1501    <property
1502      name="Cy5_AvVolpixel"
1503      title="Cy5 average intensity"
1504      description="Average intensity per pixel in color channel Cy5."
1505      column="cy5_avg"
1506      channel="2"
1507      type="float"
1508      averagemethod="arithmetic_mean"
1509    />
1510    <property
1511      name="Cy5_BGArith"
1512      title="Cy5 background (arithmetic)"
1513      description="Arithmetic average for local background in color channel Cy5."
1514      column="cy5_bg_arith"
1515      channel="2"
1516      type="float"
1517      averagemethod="arithmetic_mean"
1518    />
1519    <property
1520      name="Cy5_BGGeom"
1521      title="Cy5 background (geometric)"
1522      description="Geometric average for local background in color channel Cy5."
1523      column="cy5_bg_geom"
1524      channel="2"
1525      type="float"
1526      averagemethod="geometric_mean"
1527    />
1528    <property
1529      name="Cy5_BGMedian"
1530      title="Cy5 background (median)"
1531      description="Median average for local background in color channel Cy5."
1532      column="cy5_bg_median"
1533      channel="2"
1534      type="float"
1535      averagemethod="arithmetic_mean"
1536    />
1537    <property
1538      name="Cy5_BG_Tot"
1539      title="Cy5 background (total)"
1540      description="Total integrated background in color channel Cy5."
1541      column="cy5_bg_total"
1542      channel="2"
1543      type="float"
1544      averagemethod="arithmetic_mean"
1545    />
1546    <property
1547      name="Cy5_VolBG"
1548      title="Cy5 reduced intensity"
1549      description="Background reduced intensity of colour channel Cy5."
1550      column="cy5_reduced"
1551      channel="2"
1552      type="float"
1553      averagemethod="arithmetic_mean"
1554    />
1555    <property
1556      name="Cy5_Spotarea"
1557      title="Cy5 spot area"
1558      description="Area of spot in colour channel Cy5 in pixels."
1559      column="cy5_area"
1560      channel="2"
1561      type="float"
1562      averagemethod="arithmetic_mean"
1563    />
1564    <property
1565      name="Cy5_Satpixel"
1566      title="Cy5 saturated pixels"
1567      description="Number of saturated pixel in color channel Cy5."
1568      column="cy5_saturated"
1569      channel="2"
1570      type="float"
1571      averagemethod="arithmetic_mean"
1572    />
1573    <property
1574      name="Rep_vol_BG2"
1575      title="Background reduced volume"
1576      description="Average of background reduced volume for onchip replicas (when calculated)."
1577      column="rep_vol"
1578      type="float"
1579      averagemethod="arithmetic_mean"
1580    />
1581    <property
1582      name="RatioCy5Cy3"
1583      title="Direct ratio"
1584      description="Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )."
1585      column="ratio"
1586      type="float"
1587      averagemethod="geometric_mean"
1588    />
1589    <property
1590      name="Directional_RatioCy5Cy3"
1591      title="Directional ratio"
1592      description="Directional ratio: if Ratio &gt; 1 then Directional = Ratio, if Ratio &gt; 1 then Directional = -1/Ratio."
1593      column="directional_ratio"
1594      type="float"
1595      averagemethod="geometric_mean"
1596    />
1597    <property
1598      name="Log2_RatioCy5Cy3"
1599      title="Log2 ratio"
1600      description="Log2 ratio: log2 (Ratio-Cy5/Cy3)"
1601      column="log2_ratio"
1602      type="float"
1603      averagemethod="arithmetic_mean"
1604    />
1605    <property
1606      name="Comp_ChannelCy3"
1607      title="Cy53 normalised intensity"
1608      description="Normalised intensity of Cy3_Vol-BG."
1609      column="cy3_normalised"
1610      channel="1"
1611      type="float"
1612      averagemethod="arithmetic_mean"
1613    />
1614    <property
1615      name="Comp_ChannelCy5"
1616      title="Cy5 normalised intensity"
1617      description="Normalised intensity of Cy5_Vol-BG."
1618      column="cy5_normalised"
1619      channel="2"
1620      type="float"
1621      averagemethod="arithmetic_mean"
1622    />
1623    <property
1624      name="Comp_RatioCy5Cy3"
1625      title="Compensated ratio"
1626      description="Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 )."
1627      column="compensated_ratio"
1628      type="float"
1629      averagemethod="geometric_mean"
1630    />
1631    <property
1632      name="Comp_Directional_RatioCy5Cy3"
1633      title="Compensated directional ratio"
1634      description="Compensated directional ratio: if Comp_Ratio &gt; 1 then Directional = Ratio, if Ratio &lt; 1 then Directional = -1/Ratio."
1635      column="comp_dir_ratio"
1636      type="float"
1637      averagemethod="geometric_mean"
1638    />
1639    <property
1640      name="Comp_Log2_Ratio"
1641      title="Compensated log2 ratio"
1642      description="Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3)."
1643      column="comp_log2_ratio"
1644      type="float"
1645      averagemethod="arithmetic_mean"
1646    />
1647    <property
1648      name="Comment"
1649      title="Comment"
1650      description="Additional description of spot."
1651      column="comment"
1652      type="string"
1653      averagemethod="none"
1654    />
1655    <property
1656      name="SNRtot"
1657      title="Squared average SNR"
1658      description="Squared average of Cy5_SNR and Cy3_SNR."
1659      column="snr_tot"
1660      type="float"
1661      averagemethod="geometric_mean"
1662    />
1663    <property
1664      name="SNRtot_Score"
1665      title="Squared average score SNR"
1666      description="Squared average of Cy5_%SNR and Cy3_%SNR."
1667      column="snr_tot_score"
1668      type="float"
1669      averagemethod="geometric_mean"
1670    />
1671    <property
1672      name="SNRGS"
1673      title="Saturated pixel"
1674      description="Number of saturated pixel in both colors (logical or)."
1675      column="sat_pixels"
1676      type="float"
1677      averagemethod="arithmetic_mean"
1678    />
1679    <property
1680      name="Replicas"
1681      title="Replicas"
1682      description="Replicas"
1683      column="replicas"
1684      type="float"
1685      averagemethod="none"
1686    />
1687    <property
1688      name="Regulation"
1689      title="Regulation"
1690      description="If Flag = SNR1 then Regulation=&gt;Down; if Flag = SNR2 then Regulation=&gt;up; if Flag = SNR1 AND SNR2 then Regulation=>&gt;weak; else Regulation = Ratio-Cy5/Cy3."
1691      column="regulation"
1692      type="string"
1693      averagemethod="none"
1694    />
1695    <property
1696      name="GroupName"
1697      title="Group name"
1698      description="Group name for this spot."
1699      column="group_name"
1700      type="string"
1701      averagemethod="none"
1702    />
1703    <property
1704      name="MedianRatios"
1705      title="Median of ratios"
1706      description="Median of ratios (Cy5/Cy3) from all pixel in this spot."
1707      column="median_ratios"
1708      type="float"
1709      averagemethod="geometric_mean"
1710    />
1711    <property
1712      name="MedianRatiosSDev"
1713      title="Median of ratios (sdev%)"
1714      description="Standard deviation of Median of ratios in percent."
1715      column="median_ratios_sdev"
1716      type="float"
1717      averagemethod="arithmetic_mean"
1718    />
1719    <property
1720      name="RatioMedians"
1721      title="Ratio of medians"
1722      description="Ratio of Medians (Cy5/Cy3) from all pixel in this spot."
1723      column="ratio_medians"
1724      type="float"
1725      averagemethod="geometric_mean"
1726    />
1727    <property
1728      name="RatioMediansSDev"
1729      title="Ratio of medians (sdev%)"
1730      description="Standard deviation of Ratio of medians in percent."
1731      column="ratio_medians_sdev"
1732      type="float"
1733      averagemethod="arithmetic_mean"
1734    />
1735    <intensity-formula
1736      name="Volume"
1737      title="Volume"
1738      description="Total integrated signal intensity"
1739      >
1740      <formula 
1741        channel="1"
1742        expression="raw('Cy3_Volume')"
1743      />
1744      <formula 
1745        channel="2"
1746        expression="raw('Cy5_Volume')"
1747      />
1748    </intensity-formula>
1749    <intensity-formula
1750      name="VolBG"
1751      title="Reduced intensity"
1752      description="Background reduced intensity"
1753      >
1754      <formula 
1755        channel="1"
1756        expression="raw('Cy3_VolBG')"
1757      />
1758      <formula 
1759        channel="2"
1760        expression="raw('Cy5_VolBG')"
1761      />
1762    </intensity-formula>
1763  </raw-data-type>
1764
1765  <raw-data-type
1766    id="genetac"
1767    channels="2"
1768    name="GeneTAC"
1769    table="RawDataGeneTac"
1770    >
1771    <property
1772      name="medCy3"
1773      title="Signal median Cy3"
1774      description="Median of Cy3 signal intensity."
1775      column="med_cy3"
1776      channel="1"
1777      type="float"
1778      averagemethod="arithmetic_mean"
1779    />
1780    <property
1781      name="medCy5"
1782      title="Signal median Cy5"
1783      description="Median of Cy5 signal intensity."
1784      column="med_cy5"
1785      channel="2"
1786      type="float"
1787      averagemethod="arithmetic_mean"
1788    />
1789    <property
1790      name="medRatio"
1791      title="Signal median ratio"
1792      description="Ratio of median signal."
1793      column="med_ratio"
1794      type="float"
1795      averagemethod="geometric_mean"
1796    />
1797    <property
1798      name="bgCy3"
1799      title="Background median Cy3"
1800      description="Median of background intensity for Cy3."
1801      column="bg_cy3"
1802      channel="1"
1803      type="float"
1804      averagemethod="arithmetic_mean"
1805    />
1806    <property
1807      name="bgCy5"
1808      title="Background median Cy5"
1809      description="Median of background intensity for Cy5."
1810      column="bg_cy5"
1811      channel="2"
1812      type="float"
1813      averagemethod="arithmetic_mean"
1814    />
1815    <property
1816      name="bgRatio"
1817      title="Signal med ratio"
1818      description="Ratio of median background."
1819      column="bg_ratio"
1820      type="float"
1821      averagemethod="geometric_mean"
1822    />
1823    <intensity-formula
1824      name="medianfg"
1825      title="Median FG"
1826      description="Median foreground"
1827      >
1828      <formula 
1829        channel="1"
1830        expression="raw('medCy3')"
1831      />
1832      <formula 
1833        channel="2"
1834        expression="raw('medCy5')"
1835      />
1836    </intensity-formula>
1837    <intensity-formula
1838      name="median"
1839      title="Median FG - Median BG"
1840      description="Subtract median background from median foreground"
1841      >
1842      <formula 
1843        channel="1"
1844        expression="raw('medCy3') - raw('bgCy3')"
1845      />
1846      <formula 
1847        channel="2"
1848        expression="raw('medCy5') - raw('bgCy5')"
1849      />
1850    </intensity-formula>
1851  </raw-data-type>
1852 
1853  <raw-data-type
1854    id="imagene"
1855    channels="2"
1856    name="ImaGene"
1857    table="RawDataImaGene"
1858    >
1859    <property
1860      name="Field"
1861      title="Field"
1862      description="Name of a field where the spot is located."
1863      column="field"
1864      type="string"
1865      averagemethod="none"
1866    />
1867    <property
1868      name="Flag_Cy3"
1869      title="Flag cy3"
1870      description="Numeric code for the spot (0 - no flag, flag codes 1,...,7)."
1871      column="cy3_flag"
1872      channel="1"
1873      type="int"
1874      averagemethod="none"
1875    />
1876    <property
1877      name="SignalMean_Cy3"
1878      title="Mean signal cy3"
1879      description="Pixel intensity averaged over the local signal region."
1880      column="cy3_mean_signal"
1881      channel="1"
1882      type="float"
1883    />
1884    <property
1885      name="BackgroundMean_Cy3"
1886      title="Mean background cy3"
1887      description="Pixel intensity averaged over the local background region."
1888      column="cy3_mean_bg"
1889      channel="1"
1890      type="float"
1891      averagemethod="arithmetic_mean"
1892    />
1893    <property
1894      name="SignalMedian_Cy3"
1895      title="Median signal cy3"
1896      description="Median pixel intensity computed over the local signal region."
1897      column="cy3_median_signal"
1898      channel="1"
1899      type="float"
1900      averagemethod="arithmetic_mean"
1901    />
1902    <property
1903      name="BackgroundMedian_Cy3"
1904      title="Median background cy3"
1905      description="Median pixel intensity averaged over the local background region."
1906      column="cy3_median_bg"
1907      channel="1"
1908      type="float"
1909      averagemethod="arithmetic_mean"
1910    />
1911    <property
1912      name="SignalMode_Cy3"
1913      title="Mode signal cy3"
1914      description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
1915      column="cy3_mode_signal"
1916      channel="1"
1917      type="float"
1918      averagemethod="arithmetic_mean"
1919    />
1920    <property
1921      name="BackgroundMode_Cy3"
1922      title="Mode background cy3"
1923      description="Mode pixel intensity computed over the local background region."
1924      column="cy3_mode_bg"
1925      channel="1"
1926      type="float"
1927      averagemethod="arithmetic_mean"
1928    />
1929    <property
1930      name="SignalArea_Cy3"
1931      title="Signal area cy3"
1932      description="Number of pixels in the local signal region."
1933      column="cy3_area_signal"
1934      channel="1"
1935      type="int"
1936      averagemethod="arithmetic_mean"
1937    />
1938    <property
1939      name="BackgroundArea_Cy3"
1940      title="Background area cy3"
1941      description="Number of pixels in the local background region."
1942      column="cy3_area_bg"
1943      channel="1"
1944      type="int"
1945      averagemethod="arithmetic_mean"
1946    />
1947    <property
1948      name="SignalTotal_Cy3"
1949      title="Total signal cy3"
1950      description="Total pixel intensity summed over the local signal region."
1951      column="cy3_total_signal"
1952      channel="1"
1953      type="int"
1954      averagemethod="arithmetic_mean"
1955    />
1956    <property
1957      name="BackgroundTotal_Cy3"
1958      title="Total background cy3"
1959      description="Total pixel intensity summed over the local background region."
1960      column="cy3_total_bg"
1961      channel="1"
1962      type="int"
1963      averagemethod="arithmetic_mean"
1964    />
1965    <property
1966      name="ShapeRegularity_Cy3"
1967      title="Shape regularity cy3"
1968      description="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity."
1969      column="cy3_shape"
1970      channel="1"
1971      type="float"
1972      averagemethod="geometric_mean"
1973    />
1974    <property
1975      name="IgnoredArea_Cy3"
1976      title="Ignored area cy3"
1977      description="Area of ignored regions directly neighboring (touching) the signal area is computed."
1978      column="cy3_area_ignored"
1979      channel="1"
1980      type="int"
1981      averagemethod="arithmetic_mean"
1982    />
1983    <property
1984      name="SpotArea_Cy3"
1985      title="Spot area cy3"
1986      description="Signal Area plus Ignored Area."
1987      column="cy3_area_spot"
1988      channel="1"
1989      type="int"
1990      averagemethod="arithmetic_mean"
1991    />
1992    <property
1993      name="IgnoredMedian_Cy3"
1994      title="Median ignored cy3"
1995      description="Median pixel intensity computed over the local ignored region."
1996      column="cy3_median_ignored"
1997      channel="1"
1998      type="float"
1999      averagemethod="arithmetic_mean"
2000    />
2001    <property
2002      name="AreaToPerimeter_Cy3"
2003      title="Area to perimeter cy3"
2004      description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
2005      column="cy3_area_perimeter"
2006      channel="1"
2007      type="float"
2008      averagemethod="arithmetic_mean"
2009    />
2010    <property
2011      name="OpenPerimeter_Cy3"
2012      title="Open perimeter cy3"
2013      description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2014      column="cy3_open_perimeter"
2015      channel="1"
2016      type="float"
2017      averagemethod="arithmetic_mean"
2018    />
2019    <property
2020      name="XCoord_Cy3"
2021      title="X coordinate cy3"
2022      description="X coordinate (in pixels) of grid circle corresponding to the spot."
2023      column="cy3_x"
2024      channel="1"
2025      type="float"
2026      averagemethod="none"
2027    />
2028    <property
2029      name="YCoord_Cy3"
2030      title="Y coordinate cy3"
2031      description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2032      column="cy3_y"
2033      channel="1"
2034      type="float"
2035      averagemethod="none"
2036    />
2037    <property
2038      name="Diameter_Cy3"
2039      title="Diameter cy3"
2040      description="Diameter (in pixels) of grid circle corresponding to the spot."
2041      column="cy3_diameter"
2042      channel="1"
2043      type="int"
2044      averagemethod="arithmetic_mean"
2045    />
2046    <property
2047      name="PositionOffset_Cy3"
2048      title="Position offset cy3"
2049      description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2050      column="cy3_offset"
2051      channel="1"
2052      type="float"
2053      averagemethod="none"
2054    />
2055    <property
2056      name="OffsetX_Cy3"
2057      title="X offset cy3"
2058      description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2059      column="cy3_offset_x"
2060      channel="1"
2061      type="float"
2062      averagemethod="none"
2063    />
2064    <property
2065      name="OffsetY_Cy3"
2066      title="Y offset cy3"
2067      description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2068      column="cy3_offset_y"
2069      channel="1"
2070      type="float"
2071      averagemethod="none"
2072    />
2073    <property
2074      name="ExpectedX_Cy3"
2075      title="X expected cy3"
2076      description="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2077      column="cy3_x_expected"
2078      channel="1"
2079      type="float"
2080      averagemethod="none"
2081    />
2082    <property
2083      name="ExpectedY_Cy3"
2084      title="Y expected cy3"
2085      description="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2086      column="cy3_y_expected"
2087      channel="1"
2088      type="float"
2089      averagemethod="none"
2090    />
2091    <property
2092      name="CMX_Cy3"
2093      title="CM X coordinate cy3"
2094      description="X coordinate of the center of the mass of spot's signal region."
2095      column="cy3_x_cm"
2096      channel="1"
2097      type="float"
2098      averagemethod="none"
2099    />
2100    <property
2101      name="CMY_Cy3"
2102      title="CM Y coordinate cy3"
2103      description="Y coordinate of the center of the mass of spot's signal region."
2104      column="cy3_y_cm"
2105      channel="1"
2106      type="float"
2107      averagemethod="none"
2108    />
2109    <property
2110      name="CMOffset_Cy3"
2111      title="CM offset cy3"
2112      description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2113      column="cy3_offset_cm"
2114      channel="1"
2115      type="float"
2116      averagemethod="none"
2117    />
2118    <property
2119      name="CMOffsetX_Cy3"
2120      title="CM X offset cy3"
2121      description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2122      column="cy3_offset_x_cm"
2123      channel="1"
2124      type="float"
2125      averagemethod="none"
2126    />
2127    <property
2128      name="CMOffsetY_Cy3"
2129      title="CM Y offset cy3"
2130      description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2131      column="cy3_offset_y_cm"
2132      channel="1"
2133      type="float"
2134      averagemethod="none"
2135    />
2136    <property
2137      name="MinDiam_Cy3"
2138      title="Min diameter cy3"
2139      description="Diameter of the circle inscribed into the spot's signal region."
2140      column="cy3_diameter_min"
2141      channel="1"
2142      type="float"
2143      averagemethod="arithmetic_mean"
2144    />
2145    <property
2146      name="MaxDiam_Cy3"
2147      title="Max diameter cy3"
2148      description="Diameter of the circle, the spot's signal region can be inscribed in."
2149      column="cy3_diameter_max"
2150      channel="1"
2151      type="float"
2152      averagemethod="arithmetic_mean"
2153    />
2154    <property
2155      name="Control_Cy3"
2156      title="Control cy3"
2157      description="Name of a control type for current spot (no name means the spot is not a control spot)."
2158      column="cy3_control"
2159      channel="1"
2160      type="string"
2161      averagemethod="none"
2162    />
2163    <property
2164      name="FailedControl_Cy3"
2165      title="Failed control cy3"
2166      description="0 if the control passed all tests, 1 if at least one of the tests failed."
2167      column="cy3_control_failed"
2168      channel="1"
2169      type="boolean"
2170      averagemethod="none"
2171    />
2172    <property
2173      name="BackgroundContaminationPresent_Cy3"
2174      title="Bg contamination cy3"
2175      description="0 if the spot passed background contamination test, 1 if it did not."
2176      column="cy3_bg_contamination"
2177      channel="1"
2178      type="boolean"
2179      averagemethod="none"
2180    />
2181    <property
2182      name="SignalContaminationPresent_Cy3"
2183      title="Signal contamination cy3"
2184      description="0 if the spot passed signal contamination test, 1 if it did not."
2185      column="cy3_signal_contamination"
2186      channel="1"
2187      type="boolean"
2188      averagemethod="none"
2189    />
2190    <property
2191      name="IgnoredFailed_Cy3"
2192      title="Ignored % failed cy3"
2193      description="0 if the spot passed ignored percentage test, 1 if it did not."
2194      column="cy3_ignored_failed"
2195      channel="1"
2196      type="boolean"
2197      averagemethod="none"
2198    />
2199    <property
2200      name="OpenPerimeterFailed_Cy3"
2201      title="Open perimeter failed cy3"
2202      description="0 if the spot passed open perimeter test, 1 if it did not."
2203      column="cy3_perimeter_failed"
2204      channel="1"
2205      type="boolean"
2206      averagemethod="none"
2207    />
2208    <property
2209      name="ShapeRegularityFailed_Cy3"
2210      title="Shape regularity failed cy3"
2211      description="0 if the spot passed shape regularity test, 1 if it did not."
2212      column="cy3_shape_failed"
2213      channel="1"
2214      type="boolean"
2215      averagemethod="none"
2216    />
2217    <property
2218      name="PerimToAreaFailed_Cy3"
2219      title="Perimeter to area failed cy3"
2220      description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2221      column="cy3_areapm_failed"
2222      channel="1"
2223      type="boolean"
2224      averagemethod="none"
2225    />
2226    <property
2227      name="OffsetFailed_Cy3"
2228      title="Offset failed cy3"
2229      description="0 if the spot passed offset test, 1 if it did not."
2230      column="cy3_offset_failed"
2231      channel="1"
2232      type="boolean"
2233      averagemethod="none"
2234    />
2235    <property
2236      name="EmptySpot_Cy3"
2237      title="Empty spot cy3"
2238      description="1 if the spot is empty, 0 if not."
2239      column="cy3_empty_spot"
2240      channel="1"
2241      type="boolean"
2242      averagemethod="none"
2243    />
2244    <property
2245      name="NegativeSpot_Cy3"
2246      title="Negative spot cy3"
2247      description="1 if the spot was qualified as negative, 0 if it was not."
2248      column="cy3_negative_spot"
2249      channel="1"
2250      type="boolean"
2251      averagemethod="none"
2252    />
2253    <property
2254      name="SelectedSpot_Cy3"
2255      title="Selected spot cy3"
2256      description="1 if the spot was selected in the software view at time of save, 0 if not."
2257      column="cy3_selected_spot"
2258      channel="1"
2259      type="boolean"
2260      averagemethod="none"
2261    />
2262    <property
2263      name="SaturatedSpot_Cy3"
2264      title="Saturated spot cy3"
2265      description="1 if the spot was qualified as saturated, 0 if it was not."
2266      column="cy3_saturated_spot"
2267      channel="1"
2268      type="boolean"
2269      averagemethod="none"
2270    />
2271    <property
2272      name="SignalMean_Cy5"
2273      title="Mean signal cy5"
2274      description="Pixel intensity averaged over the local signal region."
2275      column="cy5_mean_signal"
2276      channel="2"
2277      type="float"
2278      averagemethod="arithmetic_mean"
2279    />
2280    <property
2281      name="BackgroundMean_Cy5"
2282      title="Mean background cy5"
2283      description="Pixel intensity averaged over the local background region."
2284      column="cy5_mean_bg"
2285      channel="2"
2286      type="float"
2287      averagemethod="arithmetic_mean"
2288    />
2289    <property
2290      name="SignalMedian_Cy5"
2291      title="Median signal cy5"
2292      description="Median pixel intensity computed over the local signal region."
2293      column="cy5_median_signal"
2294      channel="2"
2295      type="float"
2296      averagemethod="arithmetic_mean"
2297    />
2298    <property
2299      name="BackgroundMedian_Cy5"
2300      title="Median background cy5"
2301      description="Median pixel intensity averaged over the local background region."
2302      column="cy5_median_bg"
2303      channel="2"
2304      type="float"
2305      averagemethod="arithmetic_mean"
2306    />
2307    <property
2308      name="SignalMode_Cy5"
2309      title="Mode signal cy5"
2310      description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
2311      column="cy5_mode_signal"
2312      channel="2"
2313      type="float"
2314      averagemethod="arithmetic_mean"
2315    />
2316    <property
2317      name="BackgroundMode_Cy5"
2318      title="Mode background cy5"
2319      description="Mode pixel intensity computed over the local background region."
2320      column="cy5_mode_bg"
2321      channel="2"
2322      type="float"
2323      averagemethod="arithmetic_mean"
2324    />
2325    <property
2326      name="SignalArea_Cy5"
2327      title="Signal area cy5"
2328      description="Number of pixels in the local signal region."
2329      column="cy5_area_signal"
2330      channel="2"
2331      type="int"
2332      averagemethod="arithmetic_mean"
2333    />
2334    <property
2335      name="BackgroundArea_Cy5"
2336      title="Background area cy5"
2337      description="Number of pixels in the local background region."
2338      column="cy5_area_bg"
2339      channel="2"
2340      type="int"
2341      averagemethod="arithmetic_mean"
2342    />
2343    <property
2344      name="SignalTotal_Cy5"
2345      title="Total signal cy5"
2346      description="Total pixel intensity summed over the local signal region."
2347      column="cy5_total_signal"
2348      channel="2"
2349      type="int"
2350      averagemethod="arithmetic_mean"
2351    />
2352    <property
2353      name="BackgroundTotal_Cy5"
2354      title="Total background cy5"
2355      description="Total pixel intensity summed over the local background region."
2356      column="cy5_total_bg"
2357      channel="2"
2358      type="int"
2359      averagemethod="arithmetic_mean"
2360    />
2361    <property
2362      name="ShapeRegularity_Cy5"
2363      title="Shape regularity cy5"
2364      description="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity."
2365      column="cy5_shape"
2366      channel="2"
2367      type="float"
2368      averagemethod="arithmetic_mean"
2369    />
2370    <property
2371      name="IgnoredArea_Cy5"
2372      title="Ignored area cy5"
2373      description="Area of ignored regions directly neighboring (touching) the signal area is computed."
2374      column="cy5_area_ignored"
2375      channel="2"
2376      type="int"
2377      averagemethod="arithmetic_mean"
2378    />
2379    <property
2380      name="SpotArea_Cy5"
2381      title="Spot area cy5"
2382      description="Signal Area plus Ignored Area."
2383      column="cy5_area_spot"
2384      channel="2"
2385      type="int"
2386      averagemethod="arithmetic_mean"
2387    />
2388    <property
2389      name="IgnoredMedian_Cy5"
2390      title="Median ignored cy5"
2391      description="Median pixel intensity computed over the local ignored region."
2392      column="cy5_median_ignored"
2393      channel="2"
2394      type="float"
2395      averagemethod="arithmetic_mean"
2396    />
2397    <property
2398      name="AreaToPerimeter_Cy5"
2399      title="Area to perimeter cy5"
2400      description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
2401      column="cy5_area_perimeter"
2402      channel="2"
2403      type="float"
2404      averagemethod="arithmetic_mean"
2405    />
2406    <property
2407      name="OpenPerimeter_Cy5"
2408      title="Open perimeter cy5"
2409      description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2410      column="cy5_open_perimeter"
2411      channel="2"
2412      type="float"
2413      averagemethod="arithmetic_mean"
2414    />
2415    <property
2416      name="XCoord_Cy5"
2417      title="X coordinate cy5"
2418      description="X coordinate (in pixels) of grid circle corresponding to the spot."
2419      column="cy5_x"
2420      channel="2"
2421      type="float"
2422      averagemethod="none"
2423    />
2424    <property
2425      name="YCoord_Cy5"
2426      title="Y coordinate cy5"
2427      description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2428      column="cy5_y"
2429      channel="2"
2430      type="float"
2431      averagemethod="none"
2432    />
2433    <property
2434      name="Diameter_Cy5"
2435      title="Diameter cy5"
2436      description="Diameter (in pixels) of grid circle corresponding to the spot."
2437      column="cy5_diameter"
2438      channel="2"
2439      type="int"
2440      averagemethod="arithmetic_mean"
2441    />
2442    <property
2443      name="PositionOffset_Cy5"
2444      title="Position offset cy5"
2445      description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2446      column="cy5_offset"
2447      channel="2"
2448      type="float"
2449      averagemethod="none"
2450    />
2451    <property
2452      name="OffsetX_Cy5"
2453      title="X offset cy5"
2454      description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2455      column="cy5_offset_x"
2456      channel="2"
2457      type="float"
2458      averagemethod="none"
2459    />
2460    <property
2461      name="OffsetY_Cy5"
2462      title="Y offset cy5"
2463      description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2464      column="cy5_offset_y"
2465      channel="2"
2466      type="float"
2467      averagemethod="none"
2468    />
2469    <property
2470      name="ExpectedX_Cy5"
2471      title="X expected cy5"
2472      description="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2473      column="cy5_x_expected"
2474      channel="2"
2475      type="float"
2476      averagemethod="none"
2477    />
2478    <property
2479      name="ExpectedY_Cy5"
2480      title="Y expected cy5"
2481      description="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column."
2482      column="cy5_y_expected"
2483      channel="2"
2484      type="float"
2485      averagemethod="none"
2486    />
2487    <property
2488      name="CMX_Cy5"
2489      title="CM X coordinate cy5"
2490      description="X coordinate of the center of the mass of spot's signal region."
2491      column="cy5_x_cm"
2492      channel="2"
2493      type="float"
2494      averagemethod="none"
2495    />
2496    <property
2497      name="CMY_Cy5"
2498      title="CM Y coordinate cy5"
2499      description="Y coordinate of the center of the mass of spot's signal region."
2500      column="cy5_y_cm"
2501      channel="2"
2502      type="float"
2503      averagemethod="none"
2504    />
2505    <property
2506      name="CMOffset_Cy5"
2507      title="CM offset cy5"
2508      description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2509      column="cy5_offset_cm"
2510      channel="2"
2511      type="float"
2512      averagemethod="none"
2513    />
2514    <property
2515      name="CMOffsetX_Cy5"
2516      title="CM X offset cy5"
2517      description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2518      column="cy5_offset_x_cm"
2519      channel="2"
2520      type="float"
2521      averagemethod="none"
2522    />
2523    <property
2524      name="CMOffsetY_Cy5"
2525      title="CM Y offset cy5"
2526      description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2527      column="cy5_offset_y_cm"
2528      channel="2"
2529      type="float"
2530      averagemethod="none"
2531    />
2532    <property
2533      name="MinDiam_Cy5"
2534      title="Min diameter cy5"
2535      description="Diameter of the circle inscribed into the spot's signal region."
2536      column="cy5_diameter_min"
2537      channel="2"
2538      type="float"
2539      averagemethod="arithmetic_mean"
2540    />
2541    <property
2542      name="MaxDiam_Cy5"
2543      title="Max diameter cy5"
2544      description="Diameter of the circle, the spot's signal region can be inscribed in."
2545      column="cy5_diameter_max"
2546      channel="2"
2547      type="float"
2548      averagemethod="arithmetic_mean"
2549    />
2550    <property
2551      name="Control_Cy5"
2552      title="Control cy5"
2553      description="Name of a control type for current spot (no name means the spot is not a control spot)."
2554      column="cy5_control"
2555      channel="2"
2556      type="string"
2557      averagemethod="none"
2558    />
2559    <property
2560      name="FailedControl_Cy5"
2561      title="Failed control cy5"
2562      description="0 if the control passed all tests, 1 if at least one of the tests failed."
2563      column="cy5_control_failed"
2564      channel="2"
2565      type="boolean"
2566      averagemethod="none"
2567    />
2568    <property
2569      name="BackgroundContaminationPresent_Cy5"
2570      title="Bg contamination cy5"
2571      description="0 if the spot passed background contamination test, 1 if it did not."
2572      column="cy5_bg_contamination"
2573      channel="2"
2574      type="boolean"
2575      averagemethod="none"
2576    />
2577    <property
2578      name="SignalContaminationPresent_Cy5"
2579      title="Signal contamination cy5"
2580      description="0 if the spot passed signal contamination test, 1 if it did not."
2581      column="cy5_signal_contamination"
2582      channel="2"
2583      type="boolean"
2584      averagemethod="none"
2585    />
2586    <property
2587      name="IgnoredFailed_Cy5"
2588      title="Ignored % failed cy5"
2589      description="0 if the spot passed ignored percentage test, 1 if it did not."
2590      column="cy5_ignored_failed"
2591      channel="2"
2592      type="boolean"
2593      averagemethod="none"
2594    />
2595    <property
2596      name="OpenPerimeterFailed_Cy5"
2597      title="Open perimeter failed cy5"
2598      description="0 if the spot passed open perimeter test, 1 if it did not."
2599      column="cy5_perimeter_failed"
2600      channel="2"
2601      type="boolean"
2602      averagemethod="none"
2603    />
2604    <property
2605      name="ShapeRegularityFailed_Cy5"
2606      title="Shape regularity failed cy5"
2607      description="0 if the spot passed shape regularity test, 1 if it did not."
2608      column="cy5_shape_failed"
2609      channel="2"
2610      type="boolean"
2611      averagemethod="none"
2612    />
2613    <property
2614      name="PerimToAreaFailed_Cy5"
2615      title="Perimeter to area failed cy5"
2616      description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2617      column="cy5_areapm_failed"
2618      channel="2"
2619      type="boolean"
2620      averagemethod="none"
2621    />
2622    <property
2623      name="OffsetFailed_Cy5"
2624      title="Offset failed cy5"
2625      description="0 if the spot passed offset test, 1 if it did not."
2626      column="cy5_offset_failed"
2627      channel="2"
2628      type="boolean"
2629      averagemethod="none"
2630    />
2631    <property
2632      name="EmptySpot_Cy5"
2633      title="Empty spot cy5"
2634      description="1 if the spot is empty, 0 if not."
2635      column="cy5_empty_spot"
2636      channel="2"
2637      type="boolean"
2638      averagemethod="none"
2639    />
2640    <property
2641      name="NegativeSpot_Cy5"
2642      title="Negative spot cy5"
2643      description="1 if the spot was qualified as negative, 0 if it was not."
2644      column="cy5_negative_spot"
2645      channel="2"
2646      type="boolean"
2647      averagemethod="none"
2648    />
2649    <property
2650      name="SelectedSpot_Cy5"
2651      title="Selected spot cy5"
2652      description="1 if the spot was selected in the software view at time of save, 0 if not."
2653      column="cy5_selected_spot"
2654      channel="2"
2655      type="boolean"
2656      averagemethod="none"
2657    />
2658    <property
2659      name="SaturatedSpot_Cy5"
2660      title="Saturated spot cy5"
2661      description="1 if the spot was qualified as saturated, 0 if it was not."
2662      column="cy5_saturated_spot"
2663      channel="2"
2664      type="boolean"
2665      averagemethod="none"
2666    />
2667    <intensity-formula
2668      name="mean"
2669      title="Mean FG - Mean BG"
2670      description="Subtract mean background from mean foreground"
2671      >
2672      <formula 
2673        channel="1"
2674        expression="raw('SignalMean_Cy3') - raw('BackgroundMean_Cy3')"
2675      />
2676      <formula 
2677        channel="2"
2678        expression="raw('SignalMean_Cy5') - raw('BackgroundMean_Cy5')"
2679      />
2680    </intensity-formula>
2681    <intensity-formula
2682      name="median"
2683      title="Median FG - Median BG"
2684      description="Subtract meadian background from median foreground"
2685      >
2686      <formula 
2687        channel="1"
2688        expression="raw('SignalMedian_Cy3') - raw('BackgroundMedian_Cy3')"
2689      />
2690      <formula 
2691        channel="2"
2692        expression="raw('SignalMedian_Cy5') - raw('BackgroundMedian_Cy5')"
2693      />
2694    </intensity-formula>
2695    <intensity-formula
2696      name="medianmean"
2697      title="Median FG - Mean BG"
2698      description="Subtract mean background from median foreground"
2699      >
2700      <formula 
2701        channel="1"
2702        expression="raw('SignalMedian_Cy3') - raw('BackgroundMean_Cy3')"
2703      />
2704      <formula 
2705        channel="2"
2706        expression="raw('SignalMedian_Cy5') - raw('BackgroundMean_Cy5')"
2707      />
2708    </intensity-formula>
2709    <intensity-formula
2710      name="meanmedian"
2711      title="Mean FG - Median BG"
2712      description="Subtract median background from mean foreground"
2713      >
2714      <formula 
2715        channel="1"
2716        expression="raw('SignalMean_Cy3') - raw('BackgroundMedian_Cy3')"
2717      />
2718      <formula 
2719        channel="2"
2720        expression="raw('SignalMean_Cy5') - raw('BackgroundMedian_Cy5')"
2721      />
2722    </intensity-formula>
2723    <intensity-formula
2724      name="meanfg"
2725      title="Mean FG"
2726      description="Mean foreground"
2727      >
2728      <formula 
2729        channel="1"
2730        expression="raw('SignalMean_Cy3')"
2731      />
2732      <formula 
2733        channel="2"
2734        expression="raw('SignalMean_Cy5')"
2735      />
2736    </intensity-formula>
2737    <intensity-formula
2738      name="medianfg"
2739      title="Median FG"
2740      description="Median foreground"
2741      >
2742      <formula 
2743        channel="1"
2744        expression="raw('SignalMedian_Cy3')"
2745      />
2746      <formula 
2747        channel="2"
2748        expression="raw('SignalMedian_Cy5')"
2749      />
2750    </intensity-formula>
2751    <intensity-formula
2752      name="medianfgmeanmedianbg"
2753      title="Median FG - Mean(Median BG)"
2754      description="Subtract mean of median backgrounds from median foreground"
2755      >
2756      <formula 
2757        channel="1"
2758        expression="raw('SignalMedian_Cy3') - mean('BackgroundMedian_Cy3')"
2759      />
2760      <formula 
2761        channel="2"
2762        expression="raw('SignalMedian_Cy5') - mean('BackgroundMedian_Cy5')"
2763      />
2764    </intensity-formula>
2765    <intensity-formula
2766      name="meanfgmeanmeanbg"
2767      title="Mean FG - Mean(Mean BG)"
2768      description="Subtract mean of mean backgrounds from mean foreground"
2769      >
2770      <formula 
2771        channel="1"
2772        expression="raw('SignalMean_Cy3') - mean('BackgroundMean_Cy3')"
2773      />
2774      <formula 
2775        channel="2"
2776        expression="raw('SignalMean_Cy5') - mean('BackgroundMean_Cy5')"
2777      />
2778    </intensity-formula>
2779    <intensity-formula
2780      name="medianfgmeanmeanbg"
2781      title="Median FG - Mean(Mean BG)"
2782      description="Subtract mean of mean backgrounds from median foreground"
2783      >
2784      <formula 
2785        channel="1"
2786        expression="raw('SignalMedian_Cy3') - mean('BackgroundMean_Cy3')"
2787      />
2788      <formula 
2789        channel="2"
2790        expression="raw('SignalMedian_Cy5') - mean('BackgroundMean_Cy5')"
2791      />
2792    </intensity-formula>
2793    <intensity-formula
2794      name="meanfgmeanmedianbg"
2795      title="Mean FG - Mean(Median BG)"
2796      description="Subtract mean of median backgrounds from mean foreground"
2797      >
2798      <formula 
2799        channel="1"
2800        expression="raw('SignalMean_Cy3') - mean('BackgroundMedian_Cy3')"
2801      />
2802      <formula 
2803        channel="2"
2804        expression="raw('SignalMean_Cy5') - mean('BackgroundMedian_Cy5')"
2805      />
2806    </intensity-formula>
2807  </raw-data-type>
2808 
2809  <raw-data-type
2810    id="quantarraybiotin"
2811    channels="1"
2812    name="QuantArray Biotin"
2813    table="RawDataQuantArrayBiotin"
2814    >
2815    <property
2816      name="Number"
2817      title="Number"
2818      description="Number."
2819      column="number"
2820      type="int"
2821      averagemethod="none"
2822    />
2823    <property
2824      name="BiotinIntensity"
2825      title="Intensity"
2826      description="Mean pixel biotin foreground intensity in biotin channel."
2827      column="intensity"
2828      channel="1"
2829      type="float"
2830      averagemethod="arithmetic_mean"
2831    />
2832    <property
2833      name="BiotinBackground"
2834      title="Background"
2835      description="Mean pixel biotin background intensity in biotin channel."
2836      column="background"
2837      channel="1"
2838      type="float"
2839      averagemethod="arithmetic_mean"
2840    />
2841    <property
2842      name="BiotinDiameter"
2843      title="Diameter"
2844      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
2845      column="diameter"
2846      channel="1"
2847      type="float"
2848      averagemethod="arithmetic_mean"
2849    />
2850    <property
2851      name="BiotinArea"
2852      title="Area"
2853      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
2854      column="area"
2855      channel="1"
2856      type="int"
2857      averagemethod="arithmetic_mean"
2858    />
2859    <property
2860      name="BiotinFootprint"
2861      title="Footprint"
2862      description="The distance between the expected position of a spot and its actual measured position (in microns)."
2863      column="footprint"
2864      channel="1"
2865      type="float"
2866      averagemethod="none"
2867    />
2868    <property
2869      name="BiotinCircularity"
2870      title="Circularity"
2871      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
2872      column="cirularity"
2873      channel="1"
2874      type="float"
2875      averagemethod="none"
2876    />
2877    <property
2878      name="BiotinSpotUniformity"
2879      title="Spot uniformity"
2880      description="The uniformity of the pixels used in the spot foreground intensity calculation. This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
2881      column="uniformity"
2882      channel="1"
2883      type="float"
2884      averagemethod="none"
2885    />
2886    <property
2887      name="BiotinBkgUniformity"
2888      title="Background uniformity"
2889      description="The uniformity of the pixels used in the background intensity calculation."
2890      column="bg_uniformity"
2891      channel="1"
2892      type="float"
2893      averagemethod="none"
2894    />
2895    <property
2896      name="BiotinSignalNoiseRatio"
2897      title="Signal noise ratio"
2898      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
2899      column="snr"
2900      channel="1"
2901      type="float"
2902      averagemethod="geometric_mean"
2903    />
2904    <property
2905      name="BiotinConfidence"
2906      title="Confidence"
2907      description="Confidence."
2908      column="confidence"
2909      channel="1"
2910      type="int"
2911      averagemethod="none"
2912    />
2913    <property
2914      name="IgnoreFilter"
2915      title="Ignore filter"
2916      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2917      column="ignore_filter"
2918      type="int"
2919      averagemethod="none"
2920    />
2921    <property
2922      name="BiotinRatio"
2923      title="Ratio"
2924      description="The portion of the overall spot fluorescence contributed by biotin channel (normalized so that biotin channel contribution equals 1)."
2925      column="ratio"
2926      channel="1"
2927      type="int"
2928      averagemethod="geometric_mean"
2929    />
2930    <property
2931      name="BiotinPercent"
2932      title="Percent"
2933      description="The portion of the overall spot fluorescence contributed by biotin channel (in percent)."
2934      column="precent"
2935      channel="1"
2936      type="float"
2937      averagemethod="arithmetic_mean"
2938    />
2939    <property
2940      name="BiotinDiameterFilter"
2941      title="Diameter filter"
2942      description="Biotin diameter filter."
2943      column="diameter_filter"
2944      type="int"
2945      averagemethod="none"
2946    />
2947    <property
2948      name="BiotinAreaFilter"
2949      title="Area filter"
2950      description="Biotin area filter."
2951      column="area_filter"
2952      type="int"
2953      averagemethod="none"
2954    />
2955    <property
2956      name="BiotinFootprintFilter"
2957      title="Footprint filter"
2958      description="Biotin footprint filter."
2959      column="footprint_filter"
2960      type="int"
2961      averagemethod="none"
2962    />
2963    <property
2964      name="BiotinCircularityFilter"
2965      title="Circularity filter"
2966      description="Biotin circularity filter."
2967      column="circularity_filter"
2968      type="int"
2969      averagemethod="none"
2970    />
2971    <property
2972      name="BiotinSpotUniformityFilter"
2973      title="Spot uniformity filter"
2974      description="Biotin spot uniformity filter."
2975      column="uniformity_filter"
2976      type="int"
2977      averagemethod="none"
2978    />
2979    <property
2980      name="BiotinBkgUniformityFilter"
2981      title="Background uniformity filter"
2982      description="Biotin background uniformity filter."
2983      column="bg_uniformity_filter"
2984      type="int"
2985      averagemethod="none"
2986    />
2987    <property
2988      name="BiotinSignalNoiseRatioFilter"
2989      title="Signal noise ratio filter"
2990      description="Biotin signal noise ratio filter."
2991      column="snr_filter"
2992      type="int"
2993    />
2994    <property
2995      name="BiotinReplicateFilter"
2996      title="Replicate filter"
2997      description="Biotin replicate filter."
2998      column="replicate_filter"
2999      type="int"
3000      averagemethod="none"
3001    />
3002    <intensity-formula
3003      name="meanfg"
3004      title="Mean FG"
3005      description="Mean foreground intensity"
3006      >
3007      <formula 
3008        channel="1"
3009        expression="raw('intensity')"
3010      />
3011    </intensity-formula>
3012    <intensity-formula
3013      name="mean"
3014      title="Mean FG - Mean BG"
3015      description="Subtract mean background from mean foreground"
3016      >
3017      <formula 
3018        channel="1"
3019        expression="raw('BiotinIntensity') - raw('BiotinBackground')"
3020      />
3021    </intensity-formula>
3022  </raw-data-type>
3023 
3024  <raw-data-type
3025    id="quantarraycy"
3026    channels="2"
3027    name="QuantArray Cy"
3028    table="RawDataQuantArrayCy"
3029    >
3030    <property
3031      name="Cy3Intensity"
3032      title="Mean Cy3 intensity"
3033      description="Mean pixel Cy3 foreground intensity in Channel Cy3."
3034      column="cy3_mean"
3035      channel="1"
3036      type="float"
3037      averagemethod="arithmetic_mean"
3038    />
3039    <property
3040      name="Cy3Background"
3041      title="Mean Cy3 background"
3042      description="Mean pixel Cy3 background intensity in Channel Cy3."
3043      column="cy3_mean_bg"
3044      channel="1"
3045      type="float"
3046      averagemethod="arithmetic_mean"
3047    />
3048    <property
3049      name="Cy3Diameter"
3050      title="Cy3 spot diameter"
3051      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
3052      column="cy3_diameter"
3053      channel="1"
3054      type="float"
3055      averagemethod="arithmetic_mean"
3056    />
3057    <property
3058      name="Cy3Area"
3059      title="Cy3 spot area"
3060      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
3061      column="cy3_area"
3062      channel="1"
3063      type="int"
3064      averagemethod="arithmetic_mean"
3065    />
3066    <property
3067      name="Cy3Footprint"
3068      title="Cy3 footprint"
3069      description="The distance between the expected position of a spot and its actual measured position (in microns)."
3070      column="cy3_footprint"
3071      channel="1"
3072      type="float"
3073      averagemethod="none"
3074    />
3075    <property
3076      name="Cy3Circularity"
3077      title="Cy3 circularity"
3078      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
3079      column="cy3_circularity"
3080      channel="1"
3081      type="float"
3082      averagemethod="none"
3083    />
3084    <property
3085      name="Cy3SpotUniformity"
3086      title="Cy3 spot uniformity"
3087      description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
3088      column="cy3_uniformity"
3089      channel="1"
3090      type="float"
3091      averagemethod="none"
3092    />
3093    <property
3094      name="Cy3BkgUniformity"
3095      title="Cy3 background uniformity"
3096      description="The uniformity of the pixels used in the background intensity calculation."
3097      column="cy3_bg_uniformity"
3098      channel="1"
3099      type="float"
3100      averagemethod="none"
3101    />
3102    <property
3103      name="Cy3SignalNoiseRatio"
3104      title="Cy3 signal noise ratio"
3105      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
3106      column="cy3_snr"
3107      channel="1"
3108      type="float"
3109      averagemethod="geometric_mean"
3110    />
3111    <property
3112      name="Cy3Confidence"
3113      title="Cy3 confidence"
3114      description="Unused QuantArray feature, will always = 1."
3115      column="cy3_confidence"
3116      channel="2"
3117      type="int"
3118      averagemethod="none"
3119    />
3120    <property
3121      name="Cy5Intensity"
3122      title="Mean Cy5 intensity"
3123      description="Mean pixel Cy5 foreground intensity in Channel Cy5."
3124      column="cy5_mean"
3125      channel="2"
3126      type="float"
3127      averagemethod="arithmetic_mean"
3128    />
3129    <property
3130      name="Cy5Background"
3131      title="Mean Cy5 background"
3132      description="Mean pixel Cy5 background intensity in Channel Cy5."
3133      column="cy5_mean_bg"
3134      channel="2"
3135      type="float"
3136      averagemethod="arithmetic_mean"
3137    />
3138    <property
3139      name="Cy5Diameter"
3140      title="Cy5 spot diameter"
3141      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
3142      column="cy5_diameter"
3143      channel="2"
3144      type="float"
3145      averagemethod="arithmetic_mean"
3146    />
3147    <property
3148      name="Cy5Area"
3149      title="Cy5 spot area"
3150      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
3151      column="cy5_area"
3152      channel="2"
3153      type="int"
3154      averagemethod="arithmetic_mean"
3155    />
3156    <property
3157      name="Cy5Footprint"
3158      title="Cy5 footprint"
3159      description="The distance between the expected position of a spot and its actual measured position (in microns)."
3160      column="cy5_footprint"
3161      channel="2"
3162      type="float"
3163      averagemethod="none"
3164    />
3165    <property
3166      name="Cy5Circularity"
3167      title="Cy5 circularity"
3168      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
3169      column="cy5_circularity"
3170      channel="2"
3171      type="float"
3172      averagemethod="none"
3173    />
3174    <property
3175      name="Cy5SpotUniformity"
3176      title="Cy5 spot uniformity"
3177      description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
3178      column="cy5_uniformity"
3179      channel="2"
3180      type="float"
3181      averagemethod="none"
3182    />
3183    <property
3184      name="Cy5BkgUniformity"
3185      title="Cy5 background uniformity"
3186      description="The uniformity of the pixels used in the background intensity calculation."
3187      column="cy5_bg_uniformity"
3188      channel="2"
3189      type="float"
3190      averagemethod="none"
3191    />
3192    <property
3193      name="Cy5SignalNoiseRatio"
3194      title="Cy5 signal noise ratio"
3195      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
3196      column="cy5_snr"
3197      channel="2"
3198      type="float"
3199      averagemethod="geometric_mean"
3200    />
3201    <property
3202      name="Cy5Confidence"
3203      title="Cy5 confidence"
3204      description="Unused QuantArray feature, will always = 1."
3205      column="cy5_confidence"
3206      channel="2"
3207      type="int"
3208      averagemethod="none"
3209    />
3210    <property
3211      name="IgnoreFilter"
3212      title="Ignore filter"
3213      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
3214      column="ignore_filter"
3215      type="int"
3216      averagemethod="none"
3217    />
3218    <property
3219      name="Cy3Ratio"
3220      title="Cy3 ratio"
3221      description="The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1)."
3222      column="cy3_ratio"
3223      channel="1"
3224      type="float"
3225      averagemethod="geometric_mean"
3226    />
3227    <property
3228      name="Cy3Percent"
3229      title="Cy3 precent"
3230      description="The portion of the overall spot fluorescence contributed by channel Cy3 (in percent)."
3231      column="cy3_percent"
3232      channel="1"
3233      type="float"
3234    />
3235    <property
3236      name="Cy3SignalNoiseRatioFilter"
3237      title="Cy3 signal noise ratio filter"
3238      description="Cy3 signal noise ratio filter"
3239      column="cy3_snr_filter"
3240      channel="1"
3241      type="float"
3242      averagemethod="none"
3243    />
3244    <property
3245      name="Cy5Ratio"
3246      title="Cy5 ratio"
3247      description="The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1)."
3248      column="cy5_ratio"
3249      channel="2"
3250      type="float"
3251      averagemethod="geometric_mean"
3252    />
3253    <property
3254      name="Cy5Percent"
3255      title="Cy5 precent"
3256      description="The portion of the overall spot fluorescence contributed by channel Cy5 (in percent)."
3257      column="cy5_percent"
3258      channel="2"
3259      type="float"
3260      averagemethod="arithmetic_mean"
3261    />
3262    <property
3263      name="Cy5SignalNoiseRatioFilter"
3264      title="Cy5 signal noise ratio filter"
3265      description="Cy5 signal noise ratio filter"
3266      column="cy5_snr_filter"
3267      channel="2"
3268      type="float"
3269      averagemethod="none"
3270    />
3271    <property
3272      name="log_normalised"
3273      title="Normalized ratio"
3274      description="Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1"
3275      column="log_normalised"
3276      type="float"
3277      averagemethod="arithmetic_mean"
3278    />
3279    <intensity-formula
3280      name="meanfg"
3281      title="Mean FG"
3282      description="Mean foreground intensity"
3283      >
3284      <formula 
3285        channel="1"
3286        expression="raw('Cy3Intensity')"
3287      />
3288      <formula 
3289        channel="2"
3290        expression="raw('Cy5Intensity')"
3291      />
3292    </intensity-formula>
3293    <intensity-formula
3294      name="mean"
3295      title="Mean FG - Mean BG"
3296      description="Subtract mean background from mean foreground"
3297      >
3298      <formula 
3299        channel="1"
3300        expression="raw('Cy3Intensity') - raw('Cy3Background')"
3301      />
3302      <formula 
3303        channel="2"
3304        expression="raw('Cy5Intensity') - raw('Cy5Background')"
3305      />
3306    </intensity-formula>
3307  </raw-data-type>
3308 
3309  <raw-data-type
3310    id="spotfinder"
3311    channels="2"
3312    name="Spotfinder"
3313    table="RawDataSpotfinder"
3314    >
3315    <property
3316      name="intA"
3317      title="Intensity A"
3318      description="Spot intensity in channel A corrected for background."
3319      column="int_a"
3320      type="int"
3321      channel="1"
3322      averagemethod="arithmetic_mean"
3323    />
3324    <property
3325      name="intB"
3326      title="Intensity B"
3327      description="Spot intensity in channel B corrected for background."
3328      column="int_b"
3329      type="int"
3330      channel="2"
3331      averagemethod="arithmetic_mean"
3332    />
3333    <property
3334      name="meanRatio"
3335      title="Mean ratio"
3336      description="Spot mean ratio."
3337      column="mean_ratio"
3338      type="float"
3339      averagemethod="geometric_mean"
3340    />
3341    <property
3342      name="area"
3343      title="Area"
3344      description="Spot total area in pixels."
3345      column="area"
3346      type="int"
3347      averagemethod="arithmetic_mean"
3348    />
3349    <property
3350      name="saturation"
3351      title="Saturation factor"
3352      description="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration."
3353      column="saturation"
3354      type="float"
3355      averagemethod="arithmetic_mean"
3356    />
3357    <property
3358      name="medianRatio"
3359      title="Median ratio"
3360      description="Spot median ratio."
3361      column="median_ratio"
3362      type="float"
3363      averagemethod="geometric_mean"
3364    />
3365    <property
3366      name="modeRatio"
3367      title="Mode ratio"
3368      description="Spot mode ratio."
3369      column="mode_ratio"
3370      type="float"
3371      averagemethod="geometric_mean"
3372    />
3373    <property
3374      name="bgA"
3375      title="Background A"
3376      description="Spot background in channel A."
3377      column="bg_a"
3378      channel="1"
3379      type="int"
3380      averagemethod="arithmetic_mean"
3381    />
3382    <property
3383      name="bgB"
3384      title="Background B"
3385      description="Spot background in channel B."
3386      column="bg_b"
3387      channel="2"
3388      type="int"
3389      averagemethod="arithmetic_mean"
3390    />
3391    <property
3392      name="flagA"
3393      title="Flag A"
3394      description="Spot flag in channel A. This flag is set by QC filter."
3395      column="flag_a"
3396      channel="1"
3397      type="string"
3398      averagemethod="none"
3399    />
3400    <property
3401      name="flagB"
3402      title="Flag B"
3403      description="Spot flag in channel B. This flag is set by QC filter."
3404      column="flag_b"
3405      channel="2"
3406      type="string"
3407      averagemethod="none"
3408    />
3409    <property
3410      name="qcA"
3411      title="Spot QC score A"
3412      description="Spot QC score in channel A. This is a geometric mean of shape and S/N QC scores in channel A. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1."
3413      column="qc_a"
3414      channel="1"
3415      type="float"
3416      averagemethod="none"
3417    />
3418    <property
3419      name="qcB"
3420      title="Spot QC score B"
3421      description="Spot QC score in channel B. This is a geometric mean of shape and S/N QC scores in channel B. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1."
3422      column="qc_b"
3423      channel="2"
3424      type="float"
3425      averagemethod="none"
3426    />
3427    <property
3428      name="qcTotal"
3429      title="Total QC"
3430      description="Spot total QC score. This is a mean of QC scores in channels A and B."
3431      column="qc_total"
3432      type="float"
3433      averagemethod="none"
3434    />
3435    <property
3436      name="flag"
3437      title="Flag"
3438      description="Flag values are generated based on next conditions: A - the number of non-saturated pixels in spot is 0; B- number of non-saturated pixels in spot is between 30 and 50; C- number of non saturated pixels in spot is more then 50; S- fully or partially saturated spot, this is a warning flag. User should evaluate used spot area. X- spot was detected and rejected based on spot shape and spot intensity relative to surrounding background; Z- spot was not detected by the program; Y- spot background is higher than spot intensity."
3439      column="flag"
3440      type="string"
3441      averagemethod="none"
3442    />
3443    <intensity-formula
3444      name="int"
3445      title="Spot intensity"
3446      description="Spot intensity corrected for background."
3447      >
3448      <formula 
3449        channel="1"
3450        expression="raw('intA')"
3451      />
3452      <formula 
3453        channel="2"
3454        expression="raw('intB')"
3455      />
3456    </intensity-formula>
3457  </raw-data-type>
3458  <raw-data-type 
3459    id="illumina" 
3460    channels="1" 
3461    name="Illumina" 
3462    table="RawDataIllumina">
3463    <property
3464      name="MIN_Signal"
3465      title="MIN_Signal"
3466      description="Minimum intensity of the gene in the group."
3467      column="minSignal"
3468      type="float"
3469      averagemethod="arithmetic_mean"
3470    />
3471    <property
3472      name="AVG_Signal"
3473      title="AVG_Signal"
3474      description="Average intensity of the gene in the group."
3475      column="avgSignal"
3476      type="float"
3477      averagemethod="arithmetic_mean"
3478    />
3479    <property
3480      name="MAX_Signal"
3481      title="MAX_Signal"
3482      description="Maximum intensity of the gene in the group."
3483      column="maxSignal"
3484      type="float"
3485      averagemethod="arithmetic_mean" 
3486    />
3487    <property
3488      name="NARRAYS"
3489      title="NARRAYS"
3490      description="Number of arrays in the group."
3491      column="narrays"
3492      type="int"
3493      averagemethod="arithmetic_mean"
3494    />
3495    <property
3496      name="ARRAY_STDEV"
3497      title="ARRAY_STDEV"
3498      description="Standard deviation associated with array-to-array variability within the group (undefined when the group contains a single array)."
3499      column="arrayStdDev"
3500      type="float"
3501      averagemethod="arithmetic_mean"
3502    />
3503    <property
3504      name="BEAD_STDEV"
3505      title="BEAD_STDEV"
3506      description="Average standard deviation associated with bead-to-bead variability for the arrays in the group."
3507      column="beadStdDev"
3508      type="float"
3509      averagemethod="arithmetic_mean"
3510    />
3511    <property
3512      name="Avg_NBEADS"
3513      title="Avg_NBEADS"
3514      description="Average number of beads per bead type representing probes for the gene."
3515      column="avgNBeads"
3516      type="int"
3517      averagemethod="arithmetic_mean"
3518    />
3519    <property
3520      name="Detection"
3521      title="Detection"
3522      description="p-value computed from the background model characterizing chance that the target sequence signal was distinguishable from the negative controls."
3523      column="detection"
3524      type="float"
3525      averagemethod="none"
3526    />
3527    <intensity-formula
3528      name="avgSignal"
3529      title="Average signal"
3530      description="Average signal as determined by BeadStudio software."
3531      >
3532      <formula 
3533        channel="1"
3534        expression="raw('AVG_Signal')"
3535      />
3536    </intensity-formula>
3537  </raw-data-type>
3538  <raw-data-type
3539    id="cufflinks" 
3540    channels="1" 
3541    name="Cufflinks" 
3542    table="RawDataCufflinks"
3543    description="Cufflinks isoforms/gene-level expression values in FPKM tracking format">
3544    <property
3545      name="coverage"
3546      title="Coverage"
3547      description="Estimate for the absolute depth of read coverage across the object."
3548      column="coverage"
3549      type="float"
3550      averagemethod="arithmetic_mean"
3551    />
3552    <property
3553      name="fpkm"
3554      title="FPKM"
3555      description="Fragments Per Kilobase of exon per Million fragments mapped."
3556      column="fpkm"
3557      type="float"
3558      averagemethod="geometric_mean"
3559    />
3560    <property
3561      name="fpkm_lo"
3562      title="FPKM lo"
3563      description="The lower bound of the 95% confidence interval on the FPKM."
3564      column="fpkm_lo"
3565      type="float"
3566      averagemethod="geometric_mean"
3567    />
3568    <property
3569      name="fpkm_hi"
3570      title="FPKM hi"
3571      description="The upper bound of the 95% confidence interval on the FPKM."
3572      column="fpkm_hi"
3573      type="float"
3574      averagemethod="geometric_mean"
3575    />
3576    <property
3577      name="status"
3578      title="Status"
3579      description="Quantification status. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution."
3580      column="status"
3581      type="string"
3582      length="255"
3583      averagemethod="none"
3584    />
3585    <intensity-formula
3586      name="fpkm"
3587      title="FPKM"
3588      description="Fragments Per Kilobase of exon per Million fragments mapped."
3589      >
3590      <formula 
3591        channel="1"
3592        expression="raw('fpkm')"
3593      />
3594    </intensity-formula>
3595 
3596  </raw-data-type>
3597</raw-data-types>
3598
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