source: trunk/config/dist/raw-data-types.xml @ 4508

Last change on this file since 4508 was 4508, checked in by Jari Häkkinen, 13 years ago

Addresses #1106. Missed to change reference wherefrom retrive GPLv3 license text. And some other changes.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 98.7 KB
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1<?xml version="1.0" ?>
2<?xml-stylesheet type="text/xsl" href="raw-data-types.xsl"?>
3<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
4<!--
5  $Id: raw-data-types.xml 4508 2008-09-11 20:00:35Z jari $
6
7    Copyright (C) 2006 Nicklas Nordborg
8    Copyright (C) 2007 Johan Enell, Nicklas Nordborg
9
10    This file is part of BASE - BioArray Software Environment.
11    Available at http://base.thep.lu.se/
12
13    BASE is free software; you can redistribute it and/or modify it
14    under the terms of the GNU General Public License as published by
15    the Free Software Foundation; either version 3 of the License, or
16    (at your option) any later version.
17
18    BASE is distributed in the hope that it will be useful, but
19    WITHOUT ANY WARRANTY; without even the implied warranty of
20    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
21    General Public License for more details.
22
23    You should have received a copy of the GNU General Public License
24    along with BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26<raw-data-types>
27
28  <raw-data-type
29    id="genepix"
30    channels="2"
31    name="GenePix"
32    table="RawDataGenePix"
33    >
34    <property
35      name="diameter"
36      title="Spot diameter"
37      description="The diameter of the spot in µm"
38      column="diameter"
39      type="float"
40      averagemethod="none"
41    />
42    <property
43      name="ch1FgMedian"
44      title="Channel 1 foreground median"
45      description="The median of the foreground intensity in channel 1"
46      column="ch1_fg_median"
47      type="float"
48      channel="1"
49      averagemethod="arithmetic_mean"
50    />
51    <property
52      name="ch1FgMean"
53      title="Channel 1 foreground mean"
54      description="The mean of the foreground intensity in channel 1"
55      column="ch1_fg_mean"
56      type="float"
57      channel="1"
58      averagemethod="arithmetic_mean"
59    />
60    <property
61      name="ch1FgSd"
62      title="Channel 1 foreground standard deviation"
63      description="The standard deviation of the foreground intensity in channel 1"
64      column="ch1_fg_sd"
65      type="float"
66      channel="1"
67      averagemethod="arithmetic_mean"
68    />
69    <property
70      name="ch1BgMedian"
71      title="Channel 1 background median"
72      description="The median of the background intensity in channel 1"
73      column="ch1_bg_median"
74      type="float"
75      channel="1"
76      averagemethod="arithmetic_mean"
77    />
78    <property
79      name="ch1BgMean"
80      title="Channel 1 background mean"
81      description="The mean of the background intensity in channel 1"
82      column="ch1_bg_mean"
83      type="float"
84      channel="1"
85      averagemethod="arithmetic_mean"
86    />
87    <property
88      name="ch1BgSd"
89      title="Channel 1 background standard deviation"
90      description="The standard deviation of the background intensity in channel 1"
91      column="ch1_bg_sd"
92      type="float"
93      channel="1"
94      averagemethod="arithmetic_mean"
95    />
96    <property
97      name="ch1PercSd1"
98      title="% pixels &gt; 1 standard deviation above backgound"
99      description="Percentage of pixels more than 1 standard deviation
100        above the background intensity in channel 1"
101      column="ch1_perc_sd1"
102      type="int"
103      channel="1"
104      averagemethod="arithmetic_mean"
105    />
106    <property
107      name="ch1PercSd2"
108      title="% pixels &gt; 2 standard deviations above backgound"
109      description="Percentage of pixels more than 2 standard deviations
110        above the background intensity in channel 1"
111      column="ch1_perc_sd2"
112      type="int"
113      channel="1"
114      averagemethod="arithmetic_mean"
115    />
116    <property
117      name="ch1PercSat"
118      title="Percent saturated pixels"
119      description="Percentage of saturated pixels in channel 1"
120      column="ch1_perc_sat"
121      type="int"
122      channel="1"
123      averagemethod="arithmetic_mean"
124    />
125
126    <property
127      name="ch2FgMedian"
128      title="Channel 2 foreground median"
129      description="The median of the foreground intensity in channel 2"
130      column="ch2_fg_median"
131      type="float"
132      channel="2"
133      averagemethod="arithmetic_mean"
134    />
135    <property
136      name="ch2FgMean"
137      title="Channel 2 foreground mean"
138      description="The mean of the foreground intensity in channel 2"
139      column="ch2_fg_mean"
140      type="float"
141      channel="2"
142      averagemethod="arithmetic_mean"
143    />
144    <property
145      name="ch2FgSd"
146      title="Channel 2 foreground standard deviation"
147      description="The standard deviation of the foreground intensity in channel 2"
148      column="ch2_fg_sd"
149      type="float"
150      channel="2"
151      averagemethod="arithmetic_mean"
152    />
153    <property
154      name="ch2BgMedian"
155      title="Channel 2 background median"
156      description="The median of the background intensity in channel 2"
157      column="ch2_bg_median"
158      type="float"
159      channel="2"
160      averagemethod="arithmetic_mean"
161    />
162    <property
163      name="ch2BgMean"
164      title="Channel 2 background mean"
165      description="The mean of the background intensity in channel 2"
166      column="ch2_bg_mean"
167      type="float"
168      channel="2"
169      averagemethod="arithmetic_mean"
170    />
171    <property
172      name="ch2BgSd"
173      title="Channel 2 background standard deviation"
174      description="The standard deviation of the background intensity in channel 2"
175      column="ch2_bg_sd"
176      type="float"
177      channel="2"
178      averagemethod="arithmetic_mean"
179    />
180    <property
181      name="ch2PercSd1"
182      title="% pixels &gt; 1 standard deviation above backgound"
183      description="Percentage of pixels more than 1 standard deviation
184        above the background intensity in channel 2"
185      column="ch2_perc_sd1"
186      type="int"
187      channel="2"
188      averagemethod="arithmetic_mean"
189    />
190    <property
191      name="ch2PercSd2"
192      title="% pixels &gt; 2 standard deviations above backgound"
193      description="Percentage of pixels more than 2 standard deviations
194        above the background intensity in channel 2"
195      column="ch2_perc_sd2"
196      type="int"
197      channel="2"
198      averagemethod="arithmetic_mean"
199    />
200    <property
201      name="ch2PercSat"
202      title="Percent saturated pixels"
203      description="Percentage of saturated pixels in channel 2"
204      column="ch2_perc_sat"
205      type="int"
206      channel="2"
207      averagemethod="arithmetic_mean"
208    />
209
210    <property
211      name="ratiosSd"
212      title="Standard deviation of ratios"
213      description="The geometric standard deviation of the pixel intensity ratios."
214      column="ratios_sd"
215      type="float"
216      averagemethod="geometric_mean"
217    />
218    <property
219      name="rgnRatio"
220      title="Regression ratio"
221      description="The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature."
222      column="rgn_ratio"
223      type="float"
224      averagemethod="geometric_mean"
225    />
226    <property
227      name="rgnR2"
228      title="Rgn R2"
229      description="The coefficient of determination for the current regression value."
230      column="rgn_r2"
231      type="float"
232      averagemethod="geometric_mean"
233    />
234
235    <property
236      name="fgPixels"
237      title="Foreground pixels"
238      description="Number of foreground pixels"
239      column="fg_pixels"
240      type="int"
241      averagemethod="arithmetic_mean"
242    />
243    <property
244      name="bgPixels"
245      title="Background pixels"
246      description="Number of background pixels"
247      column="bg_pixels"
248      type="int"
249      averagemethod="arithmetic_mean"
250    />
251    <property
252      name="flags"
253      title="Flags"
254      description="Flags"
255      column="flags"
256      type="int"
257      averagemethod="none"
258    />
259    <property
260      name="mValue"
261      title="M value"
262      description="M value"
263      column="m_value"
264      type="float"
265      averagemethod="arithmetic_mean"
266    />
267    <property
268      name="CV"
269      title="CV"
270      description="CV"
271      column="cv"
272      type="float"
273      averagemethod="none"
274    />
275    <intensity-formula
276      name="mean"
277      title="Mean FG - Mean BG"
278      description="Subtract mean background from mean foreground"
279      >
280      <formula 
281        channel="1"
282        expression="raw('ch1FgMean') - raw('ch1BgMean')"
283      />
284      <formula 
285        channel="2"
286        expression="raw('ch2FgMean') - raw('ch2BgMean')"
287      />
288    </intensity-formula>
289    <intensity-formula
290      name="median"
291      title="Median FG - Median BG"
292      description="Subtract meadian background from median foreground"
293      >
294      <formula 
295        channel="1"
296        expression="raw('ch1FgMedian') - raw('ch1BgMedian')"
297      />
298      <formula 
299        channel="2"
300        expression="raw('ch2FgMedian') - raw('ch2BgMedian')"
301      />
302    </intensity-formula>
303    <intensity-formula
304      name="medianmean"
305      title="Median FG - Mean BG"
306      description="Subtract mean background from median foreground"
307      >
308      <formula 
309        channel="1"
310        expression="raw('ch1FgMedian') - raw('ch1BgMean')"
311      />
312      <formula 
313        channel="2"
314        expression="raw('ch2FgMedian') - raw('ch2BgMean')"
315      />
316    </intensity-formula>
317    <intensity-formula
318      name="meanmedian"
319      title="Mean FG - Median BG"
320      description="Subtract median background from mean foreground"
321      >
322      <formula 
323        channel="1"
324        expression="raw('ch1FgMean') - raw('ch1BgMedian')"
325      />
326      <formula 
327        channel="2"
328        expression="raw('ch2FgMean') - raw('ch2BgMedian')"
329      />
330    </intensity-formula>
331    <intensity-formula
332      name="meanfg"
333      title="Mean FG"
334      description="Mean foreground"
335      >
336      <formula 
337        channel="1"
338        expression="raw('ch1FgMean')"
339      />
340      <formula 
341        channel="2"
342        expression="raw('ch2FgMean')"
343      />
344    </intensity-formula>
345    <intensity-formula
346      name="medianfg"
347      title="Median FG"
348      description="Median foreground"
349      >
350      <formula 
351        channel="1"
352        expression="raw('ch1FgMedian')"
353      />
354      <formula 
355        channel="2"
356        expression="raw('ch2FgMedian')"
357      />
358    </intensity-formula>
359    <intensity-formula
360      name="medianfgmeanmedianbg"
361      title="Median FG - Mean(Median BG)"
362      description="Subtract mean of median backgrounds from median foreground"
363      >
364      <formula 
365        channel="1"
366        expression="raw('ch1FgMedian') - mean('ch1BgMedian')"
367      />
368      <formula 
369        channel="2"
370        expression="raw('ch2FgMedian') - mean('ch2BgMedian')"
371      />
372    </intensity-formula>
373    <intensity-formula
374      name="meanfgmeanmeanbg"
375      title="Mean FG - Mean(Mean BG)"
376      description="Subtract mean of mean backgrounds from mean foreground"
377      >
378      <formula 
379        channel="1"
380        expression="raw('ch1FgMean') - mean('ch1BgMean')"
381      />
382      <formula 
383        channel="2"
384        expression="raw('ch2FgMean') - mean('ch2BgMean')"
385      />
386    </intensity-formula>
387    <intensity-formula
388      name="medianfgmeanmeanbg"
389      title="Median FG - Mean(Mean BG)"
390      description="Subtract mean of mean backgrounds from median foreground"
391      >
392      <formula 
393        channel="1"
394        expression="raw('ch1FgMedian') - mean('ch1BgMean')"
395      />
396      <formula 
397        channel="2"
398        expression="raw('ch2FgMedian') - mean('ch2BgMean')"
399      />
400    </intensity-formula>
401    <intensity-formula
402      name="meanfgmeanmedianbg"
403      title="Mean FG - Mean(Median BG)"
404      description="Subtract mean of median backgrounds from mean foreground"
405      >
406      <formula 
407        channel="1"
408        expression="raw('ch1FgMean') - mean('ch1BgMedian')"
409      />
410      <formula 
411        channel="2"
412        expression="raw('ch2FgMean') - mean('ch2BgMedian')"
413      />
414    </intensity-formula>
415  </raw-data-type>
416 
417  <raw-data-type
418    id="bzscan"
419    channels="1"
420    name="BZScan"
421    table="RawDataBZScan"
422    >
423    <property
424      name="QImageConst"
425      title="Q(image,const)"
426      description="Spot intensity based on user-provided diameter and measured data."
427      column="q_image_const"
428      type="float"
429    />
430    <property
431      name="QImageVar"
432      title="Q(image,var)"
433      description="Spot intensity based on computed diameter and measured data."
434      column="q_image_var"
435      type="float"
436    />
437    <property
438      name="QFitConst"
439      title="Q(fit,const)"
440      description="Spot intensity based on user-provided diameter and theoretical fit to the data."
441      column="q_fit_const"
442      type="float"
443    />
444    <property
445      name="QFitVar"
446      title="Q(fit,var)"
447      description="Spot intensity based on computed diameter and and theoretical fit to the data."
448      column="q_fit_var"
449      type="float"
450    />
451    <property
452      name="FitCorrection"
453      title="Fit correction"
454      description="Background level by unit surface."
455      column="fit_correction"
456      type="float"
457    />
458    <property
459      name="QM"
460      title="Quality metric"
461      description="Quality metric: distance between measured data and theoretical fit."
462      column="quality_metric"
463      type="float"
464    />
465    <property
466      name="SpotQuality"
467      title="Spot quality"
468      description="Present/Absent (automatic guess)."
469      column="spot_quality"
470      type="boolean"
471    />
472    <property
473      name="OvershiningCorrection"
474      title="Overshining correction"
475      description="Correction for overshining by unit radius."
476      column="overshining"
477      type="float"
478    />
479    <intensity-formula
480      name="QImageConst"
481      title="Q(image,const)"
482      description="Spot intensity based on user-provided diameter and measured data"
483      >
484      <formula 
485        channel="1"
486        expression="raw('QImageConst')"
487      />
488    </intensity-formula>
489    <intensity-formula
490      name="QImageVar"
491      title="Q(image,var)"
492      description="Spot intensity based on computed diameter and measured data"
493      >
494      <formula 
495        channel="1"
496        expression="raw('QImageVar')"
497      />
498    </intensity-formula>
499    <intensity-formula
500      name="QFitConst"
501      title="Q(fit,const)"
502      description="Spot intensity based on user-provided diameter and theoretical fit to the data"
503      >
504      <formula 
505        channel="1"
506        expression="raw('QFitConst')"
507      />
508    </intensity-formula>
509    <intensity-formula
510      name="QFitVar"
511      title="Q(fit,var)"
512      description="Spot intensity based on computed diameter and and theoretical fit to the data"
513      >
514      <formula 
515        channel="1"
516        expression="raw('QFitVar')"
517      />
518    </intensity-formula>
519  </raw-data-type>
520 
521  <raw-data-type
522    id="aida"
523    channels="2"
524    name="AIDA"
525    table="RawDataAida"
526    >
527    <property
528      name="area"
529      title="Area"
530      description="Spot area in pixels."
531      column="area"
532      type="float"
533      averagemethod="arithmetic_mean"
534    />
535    <property
536      name="ch1Integral"
537      title="Channel 1 integral"
538      description="Integrated raw intensity of spot channel 1."
539      column="ch1_integral"
540      type="float"
541      channel="1"
542      averagemethod="arithmetic_mean"
543    />
544    <property
545      name="ch1Mean"
546      title="Channel 1 mean"
547      description="Mean (Integral/Area) channel 1."
548      column="ch1_mean"
549      type="float"
550      channel="1"
551      averagemethod="arithmetic_mean"
552    />
553    <property
554      name="ch1Median"
555      title="Channel 1 median"
556      description="Median of the raw pixel intensity of spot channel 1."
557      column="ch1_median"
558      type="float"
559      channel="1"
560      averagemethod="arithmetic_mean"
561    />
562    <property
563      name="ch1Bkg"
564      title="Channel 1 background"
565      description="Standard deviation of background channel 1."
566      column="ch1_bkg"
567      type="float"
568      channel="1"
569      averagemethod="arithmetic_mean"
570    />
571    <property
572      name="ch1Sat"
573      title="Channel 1 saturated"
574      description="Measure of saturation pixels channel 1."
575      column="ch1_sat"
576      type="float"
577      channel="1"
578      averagemethod="arithmetic_mean"
579    />
580    <property
581      name="ch1Hom"
582      title="Channel 1 homogenity"
583      description="Percentage of dot deviation from homogenous intensity distribution channel 1."
584      column="ch1_hom"
585      type="float"
586      channel="1"
587      averagemethod="arithmetic_mean"
588    />
589    <property
590      name="ch1Quality"
591      title="Channel 1 quality"
592      description="Quality flag channel 1."
593      column="ch1_quality"
594      type="boolean"
595      channel="1"
596      averagemethod="none"
597    />
598    <property
599      name="ch2Integral"
600      title="Channel 2 integral"
601      description="Integrated raw intensity of spot channel 2."
602      column="ch2_integral"
603      type="float"
604      channel="2"
605      averagemethod="arithmetic_mean"
606    />
607    <property
608      name="ch2Mean"
609      title="Channel 2 mean"
610      description="Mean (Integral/Area) channel 2."
611      column="ch2_mean"
612      type="float"
613      channel="2"
614      averagemethod="arithmetic_mean"
615    />
616    <property
617      name="ch2Median"
618      title="Channel 2 median"
619      description="Median of the raw pixel intensity of spot channel 2."
620      column="ch2_median"
621      type="float"
622      channel="2"
623      averagemethod="arithmetic_mean"
624    />
625    <property
626      name="ch2Bkg"
627      title="Channel 2 background"
628      description="Standard deviation of background channel 2."
629      column="ch2_bkg"
630      type="float"
631      channel="2"
632      averagemethod="arithmetic_mean"
633    />
634    <property
635      name="ch2Sat"
636      title="Channel 2 saturated"
637      description="Measure of saturation pixels channel 2."
638      column="ch2_sat"
639      type="float"
640      channel="2"
641      averagemethod="arithmetic_mean"
642    />
643    <property
644      name="ch2Hom"
645      title="Channel 2 homogenity"
646      description="Percentage of dot deviation from homogenous intensity distribution channel 2."
647      column="ch2_hom"
648      type="float"
649      channel="2"
650      averagemethod="arithmetic_mean"
651    />
652    <property
653      name="ch2Quality"
654      title="Channel 2 quality"
655      description="Quality flag channel 2."
656      column="ch2_quality"
657      type="boolean"
658      channel="2"
659      averagemethod="none"
660    />
661    <intensity-formula
662      name="mean"
663      title="Mean"
664      description="Mean of the raw pixel intensity (Integral/Area)"
665      >
666      <formula 
667        channel="1"
668        expression="raw('ch1Mean')"
669      />
670      <formula 
671        channel="2"
672        expression="raw('ch2Mean')"
673      />
674    </intensity-formula>
675    <intensity-formula
676      name="median"
677      title="Median"
678      description="Median of the raw pixel intensity"
679      >
680      <formula 
681        channel="1"
682        expression="raw('ch1Median')"
683      />
684      <formula 
685        channel="2"
686        expression="raw('ch2Median')"
687      />
688    </intensity-formula>
689  </raw-data-type>
690
691  <raw-data-type
692    id="agilent"
693    channels="2"
694    name="Agilent"
695    table="RawDataAgilent"
696    >
697    <property
698      name="LogRatio"
699      title="Log ratio"
700      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."
701      column="log_ratio"
702      type="float"
703      averagemethod="arithmetic_mean"
704    />
705    <property
706      name="PValueLogRatio"
707      title="P value log ratio"
708      description="Significance level of the Log Ratio computed for a feature."
709      column="pvalue_log_ratio"
710      type="float"
711      averagemethod="arithmetic_mean"
712    />
713    <property
714      name="gSurrogateUsed"
715      title="G surrogate used"
716      description="The green surrogate value used."
717      column="g_surrogate_used"
718      channel="1"
719      type="float"
720      averagemethod="none"
721    />
722    <property
723      name="rSurrogateUsed"
724      title="R surrogate used"
725      description="The red surrogate value used."
726      column="r_surrogate_used"
727      channel="2"
728      type="float"
729      averagemethod="none"
730    />
731    <property
732      name="gIsFound"
733      title="G is found"
734      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."
735      column="g_is_found"
736      channel="1"
737      type="boolean"
738      averagemethod="none"
739    />
740    <property
741      name="rIsFound"
742      title="R is found"
743      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."
744      column="r_is_found"
745      channel="2"
746      type="boolean"
747      averagemethod="none"
748    />
749    <property
750      name="gProcessedSignal"
751      title="G processed signal"
752      description="The propagated feature signal, per channel, used for computation of log ratio."
753      column="g_processed_signal"
754      channel="1"
755      type="float"
756      averagemethod="arithmetic_mean"
757    />
758    <property
759      name="rProcessedSignal"
760      title="R processed signal"
761      description="The propagated feature signal, per channel, used for computation of log ratio."
762      column="r_processed_signal"
763      channel="2"
764      type="float"
765      averagemethod="arithmetic_mean"
766    />
767    <property
768      name="gNumPixOLHi"
769      title="G high outlier pixels"
770      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."
771      column="g_high_outlier_pixels"
772      channel="1"
773      type="int"
774      averagemethod="arithmetic_mean"
775    />
776    <property
777      name="rNumPixOLHi"
778      title="R high outlier pixels"
779      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."
780      column="r_high_outlier_pixels"
781      channel="2"
782      type="int"
783      averagemethod="arithmetic_mean"
784    />
785    <property
786      name="gNumPixOLLo"
787      title="G low outlier pixels"
788      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."
789      column="g_low_outlier_pixels"
790      channel="1"
791      type="int"
792      averagemethod="arithmetic_mean"
793    />
794    <property
795      name="rNumPixOLLo"
796      title="R low outlier pixels"
797      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."
798      column="r_low_outlier_pixels"
799      channel="2"
800      type="int"
801      averagemethod="arithmetic_mean"
802    />
803    <property
804      name="gNumPix"
805      title="G pixels"
806      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."
807      column="g_pixels"
808      channel="1"
809      type="int"
810      averagemethod="arithmetic_mean"
811    />
812    <property
813      name="rNumPix"
814      title="R pixels"
815      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."
816      column="r_pixels"
817      channel="2"
818      type="int"
819      averagemethod="arithmetic_mean"
820    />
821    <property
822      name="gMeanSignal"
823      title="G mean signal"
824      description="Raw mean signal of feature in green channel."
825      column="g_mean_signal"
826      channel="1"
827      type="float"
828      averagemethod="arithmetic_mean"
829    />
830    <property
831      name="rMeanSignal"
832      title="R mean signal"
833      description="Raw mean signal of feature in red channel."
834      column="r_mean_signal"
835      channel="2"
836      type="float"
837      averagemethod="arithmetic_mean"
838    />
839    <property
840      name="gMedianSignal"
841      title="G median signal"
842      description="Raw median signal of feature in green channel."
843      column="g_median_signal"
844      channel="1"
845      type="float"
846      averagemethod="arithmetic_mean"
847    />
848    <property
849      name="rMedianSignal"
850      title="R median signal"
851      description="Raw median signal of feature in red channel."
852      column="r_median_signal"
853      channel="2"
854      type="float"
855      averagemethod="arithmetic_mean"
856    />
857    <property
858      name="gBGNumPix"
859      title="G background pixels"
860      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."
861      column="g_bg_pixels"
862      channel="1"
863      type="int"
864      averagemethod="arithmetic_mean"
865    />
866    <property
867      name="rBGNumPix"
868      title="R background pixels"
869      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."
870      column="r_bg_pixels"
871      channel="2"
872      type="int"
873      averagemethod="arithmetic_mean"
874    />
875    <property
876      name="gBGMeanSignal"
877      title="G mean background"
878      description="Mean local background signal (local to corresponding feature) computed per channel."
879      column="g_bg_mean_signal"
880      channel="1"
881      type="float"
882      averagemethod="arithmetic_mean"
883    />
884    <property
885      name="rBGMeanSignal"
886      title="R mean background"
887      description="Mean local background signal (local to corresponding feature) computed per channel."
888      column="r_bg_mean_signal"
889      channel="2"
890      type="float"
891      averagemethod="arithmetic_mean"
892    />
893    <property
894      name="gBGMedianSignal"
895      title="G median background"
896      description="Median local background signal (local to corresponding feature) computed per channel."
897      column="g_bg_median_signal"
898      channel="1"
899      type="float"
900      averagemethod="arithmetic_mean"
901    />
902    <property
903      name="rBGMedianSignal"
904      title="R median background"
905      description="Median local background signal (local to corresponding feature) computed per channel."
906      column="r_bg_median_signal"
907      channel="2"
908      type="float"
909      averagemethod="arithmetic_mean"
910    />
911    <property
912      name="gNumSatPix"
913      title="G saturated pixels"
914      description="Total number of saturated pixels per feature, computed per channel."
915      column="g_sat_pixels"
916      channel="1"
917      type="int"
918      averagemethod="arithmetic_mean"
919    />
920    <property
921      name="rNumSatPix"
922      title="R saturated pixels"
923      description="Total number of saturated pixels per feature, computed per channel."
924      column="r_sat_pixels"
925      channel="2"
926      type="int"
927      averagemethod="arithmetic_mean"
928    />
929    <property
930      name="gIsSaturated"
931      title="G is saturated"
932      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."
933      column="g_is_saturated"
934      channel="1"
935      type="boolean"
936      averagemethod="none"
937    />
938    <property
939      name="rIsSaturated"
940      title="R is saturated"
941      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."
942      column="r_is_saturated"
943      channel="2"
944      type="boolean"
945      averagemethod="none"
946    />
947    <property
948      name="PixCorrelation"
949      title="Pix correlation"
950      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."
951      column="pix_correlation"
952      type="float"
953      averagemethod="geometric_mean"
954    />
955    <property
956      name="BGPixCorrelation"
957      title="BG pix correlation"
958      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."
959      column="bg_pix_correlation"
960      type="float"
961      averagemethod="geometric_mean"
962    />
963    <property
964      name="gIsFeatNonUnifOL"
965      title="G non-uniform outlier"
966      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."
967      column="g_nonuniform_outlier"
968      channel="1"
969      type="boolean"
970      averagemethod="none"
971    />
972    <property
973      name="rIsFeatNonUnifOL"
974      title="R non-uniform outlier"
975      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."
976      column="r_nonuniform_outlier"
977      channel="2"
978      type="boolean"
979    />
980    <property
981      name="gIsBGNonUnifOL"
982      title="G bg non-uniform outlier"
983      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."
984      column="g_bg_nonuniform_outlier"
985      channel="1"
986      type="boolean"
987    />
988    <property
989      name="rIsBGNonUnifOL"
990      title="R bg non-uniform outlier"
991      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."
992      column="r_bg_nonuniform_outlier"
993      channel="2"
994      type="boolean"
995    />
996    <property
997      name="gIsFeatPopnOL"
998      title="G population outlier"
999      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."
1000      column="g_population_outlier"
1001      channel="1"
1002      type="boolean"
1003    />
1004    <property
1005      name="rIsFeatPopnOL"
1006      title="R population outlier"
1007      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."
1008      column="r_population_outlier"
1009      channel="2"
1010      type="boolean"
1011      averagemethod="none"
1012    />
1013    <property
1014      name="gIsBGPopnOL"
1015      title="G bg population outlier"
1016      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."
1017      column="g_bg_population_outlier"
1018      channel="1"
1019      type="boolean"
1020      averagemethod="none"
1021    />
1022    <property
1023      name="rIsBGPopnOL"
1024      title="R bg population outlier"
1025      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."
1026      column="r_bg_population_outlier"
1027      channel="2"
1028      type="boolean"
1029      averagemethod="none"
1030    />
1031    <property
1032      name="IsManualFlag"
1033      title="Manual flag"
1034      description="If a feature has been moved manually this flag will be set to 1."
1035      column="manual_flag"
1036      type="boolean"
1037      averagemethod="none"
1038    />
1039    <property
1040      name="gBGSubSignal"
1041      title="G net signal"
1042      description="The net green signal following the subtraction of the background from the raw mean green signal."
1043      column="g_net_signal"
1044      channel="1"
1045      type="float"
1046    />
1047    <property
1048      name="rBGSubSignal"
1049      title="R net signal"
1050      description="The net red signal following the subtraction of the background from the raw mean red signal."
1051      column="r_net_signal"
1052      channel="2"
1053      type="float"
1054      averagemethod="arithmetic_mean"
1055    />
1056    <property
1057      name="BGSubSigCorrelation"
1058      title="BG correlation"
1059      description="Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space."
1060      column="bg_correlation"
1061      type="float"
1062      averagemethod="geometric_mean"
1063    />
1064    <property
1065      name="gIsPosAndSignif"
1066      title="G > 0 and significant"
1067      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."
1068      column="g_significant"
1069      channel="1"
1070      type="boolean"
1071      averagemethod="none"
1072    />
1073    <property
1074      name="rIsPosAndSignif"
1075      title="R > 0 and significant"
1076      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."
1077      column="r_significant"
1078      channel="2"
1079      type="boolean"
1080      averagemethod="none"
1081    />
1082    <property
1083      name="gPValFeatEqBG"
1084      title="G p-value"
1085      description="P-value from t-test of significance between green Mean signal and green background."
1086      column="g_pvalue"
1087      channel="1"
1088      type="float"
1089      averagemethod="none"
1090    />
1091    <property
1092      name="rPValFeatEqBG"
1093      title="R p-value"
1094      description="P-value from t-test of significance between red Mean signal and red background."
1095      column="r_pvalue"
1096      channel="2"
1097      type="float"
1098      averagemethod="none"
1099    />
1100    <property
1101      name="gNumBGUsed"
1102      title="G background pixels"
1103      description="A count of the number of background pixels used in the green channel."
1104      column="g_numbg_used"
1105      channel="1"
1106      type="int"
1107      averagemethod="arithmetic_mean"
1108    />
1109    <property
1110      name="rNumBGUsed"
1111      title="R background pixels"
1112      description="A count of the number of background pixels used in the red channel."
1113      column="r_numbg_used"
1114      channel="2"
1115      type="int"
1116      averagemethod="arithmetic_mean"
1117    />
1118    <property
1119      name="gIsWellAboveBG"
1120      title="G well above bg"
1121      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."
1122      column="g_above_bg"
1123      channel="1"
1124      type="boolean"
1125      averagemethod="none"
1126    />
1127    <property
1128      name="rIsWellAboveBG"
1129      title="R well above bg"
1130      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."
1131      column="r_above_bg"
1132      channel="2"
1133      type="boolean"
1134      averagemethod="none"
1135    />
1136    <property
1137      name="gBGUsed"
1138      title="G bg used"
1139      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."
1140      column="g_bg_used"
1141      channel="1"
1142      type="float"
1143      averagemethod="arithmetic_mean"
1144    />
1145    <property
1146      name="rBGUsed"
1147      title="R bg used"
1148      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."
1149      column="r_bg_used"
1150      channel="2"
1151      type="float"
1152      averagemethod="arithmetic_mean"
1153    />
1154    <property
1155      name="IsNormalization"
1156      title="Normalization"
1157      description="A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used."
1158      column="is_normalization"
1159      type="boolean"
1160      averagemethod="none"
1161    />
1162    <property
1163      name="gDyeNormSignal"
1164      title="G normalized signal"
1165      description="The dye normalized signal in the green channel."
1166      column="g_normalized"
1167      channel="1"
1168      type="float"
1169      averagemethod="arithmetic_mean"
1170    />
1171    <property
1172      name="rDyeNormSignal"
1173      title="R normalized signal"
1174      description="The dye normalized signal in the green channel."
1175      column="r_normalized"
1176      channel="2"
1177      type="float"
1178      averagemethod="arithmetic_mean"
1179    />
1180    <property
1181      name="DyeNormCorrelation"
1182      title="Normalized correlation"
1183      description="Dye normalized red and green pixel correlation."
1184      column="norm_correlation"
1185      type="float"
1186      averagemethod="none"
1187    />
1188    <property
1189      name="ErrorModel"
1190      title="Error model"
1191      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."
1192      column="error_model"
1193      type="int"
1194      averagemethod="none"
1195    />
1196    <property
1197      name="xDev"
1198      title="X dev"
1199      description="Used to compute the Log Ratio PValue."
1200      column="x_dev"
1201      type="float"
1202      averagemethod="none"
1203    />
1204    <property
1205      name="gSpatialDetrendIsInFilteredSet"
1206      title="G spatial trend"
1207      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."
1208      column="g_spatial_trend"
1209      channel="1"
1210      type="boolean"
1211      averagemethod="none"
1212    />
1213    <property
1214      name="rSpatialDetrendIsInFilteredSet"
1215      title="R spatial trend"
1216      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."
1217      column="r_spatial_trend"
1218      channel="2"
1219      type="boolean"
1220      averagemethod="none"
1221    />
1222    <property
1223      name="gSpatialDetrendSurfaceValue"
1224      title="G surface value"
1225      description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1226      column="g_surface_value"
1227      channel="1"
1228      type="float"
1229      averagemethod="arithmetic_mean"
1230    />
1231    <property
1232      name="rSpatialDetrendSurfaceValue"
1233      title="R surface value"
1234      description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1235      column="r_surface_value"
1236      channel="2"
1237      type="float"
1238      averagemethod="arithmetic_mean"
1239    />
1240    <intensity-formula
1241      name="mean"
1242      title="Mean FG - Mean BG"
1243      description="Subtract mean background from mean foreground"
1244      >
1245      <formula 
1246        channel="1"
1247        expression="raw('gMeanSignal') - raw('gBGMeanSignal')"
1248      />
1249      <formula 
1250        channel="2"
1251        expression="raw('rMeanSignal') - raw('rBGMeanSignal')"
1252      />
1253    </intensity-formula>
1254    <intensity-formula
1255      name="median"
1256      title="Median FG - Median BG"
1257      description="Subtract meadian background from median foreground"
1258      >
1259      <formula 
1260        channel="1"
1261        expression="raw('gMedianSignal') - raw('gBGMedianSignal')"
1262      />
1263      <formula 
1264        channel="2"
1265        expression="raw('rMedianSignal') - raw('rBGMedianSignal')"
1266      />
1267    </intensity-formula>
1268    <intensity-formula
1269      name="medianmean"
1270      title="Median FG - Mean BG"
1271      description="Subtract mean background from median foreground"
1272      >
1273      <formula 
1274        channel="1"
1275        expression="raw('gMedianSignal') - raw('gBGMeanSignal')"
1276      />
1277      <formula 
1278        channel="2"
1279        expression="raw('rMedianSignal') - raw('rBGMeanSignal')"
1280      />
1281    </intensity-formula>
1282    <intensity-formula
1283      name="meanmedian"
1284      title="Mean FG - Median BG"
1285      description="Subtract median background from mean foreground"
1286      >
1287      <formula 
1288        channel="1"
1289        expression="raw('gMeanSignal') - raw('gBGMedianSignal')"
1290      />
1291      <formula 
1292        channel="2"
1293        expression="raw('rMeanSignal') - raw('rBGMedianSignal')"
1294      />
1295    </intensity-formula>
1296    <intensity-formula
1297      name="meanfg"
1298      title="Mean FG"
1299      description="Mean foreground"
1300      >
1301      <formula 
1302        channel="1"
1303        expression="raw('gMeanSignal')"
1304      />
1305      <formula 
1306        channel="2"
1307        expression="raw('rMeanSignal')"
1308      />
1309    </intensity-formula>
1310    <intensity-formula
1311      name="medianfg"
1312      title="Median FG"
1313      description="Median foreground"
1314      >
1315      <formula 
1316        channel="1"
1317        expression="raw('gMedianSignal')"
1318      />
1319      <formula 
1320        channel="2"
1321        expression="raw('rMedianSignal')"
1322      />
1323    </intensity-formula>
1324    <intensity-formula
1325      name="medianfgmeanmedianbg"
1326      title="Median FG - Mean(Median BG)"
1327      description="Subtract mean of median backgrounds from median foreground"
1328      >
1329      <formula 
1330        channel="1"
1331        expression="raw('gMedianSignal') - mean('gBGMedianSignal')"
1332      />
1333      <formula 
1334        channel="2"
1335        expression="raw('rMedianSignal') - mean('rBGMedianSignal')"
1336      />
1337    </intensity-formula>
1338    <intensity-formula
1339      name="meanfgmeanmeanbg"
1340      title="Mean FG - Mean(Mean BG)"
1341      description="Subtract mean of mean backgrounds from mean foreground"
1342      >
1343      <formula 
1344        channel="1"
1345        expression="raw('gMeanSignal') - mean('gBGMeanSignal')"
1346      />
1347      <formula 
1348        channel="2"
1349        expression="raw('rMeanSignal') - mean('rBGMeanSignal')"
1350      />
1351    </intensity-formula>
1352    <intensity-formula
1353      name="medianfgmeanmeanbg"
1354      title="Median FG - Mean(Mean BG)"
1355      description="Subtract mean of mean backgrounds from median foreground"
1356      >
1357      <formula 
1358        channel="1"
1359        expression="raw('gMedianSignal') - mean('gBGMeanSignal')"
1360      />
1361      <formula 
1362        channel="2"
1363        expression="raw('rMedianSignal') - mean('rBGMeanSignal')"
1364      />
1365    </intensity-formula>
1366    <intensity-formula
1367      name="meanfgmeanmedianbg"
1368      title="Mean FG - Mean(Median BG)"
1369      description="Subtract mean of median backgrounds from mean foreground"
1370      >
1371      <formula 
1372        channel="1"
1373        expression="raw('gMeanSignal') - mean('gBGMedianSignal')"
1374      />
1375      <formula 
1376        channel="2"
1377        expression="raw('rMeanSignal') - mean('rBGMedianSignal')"
1378      />
1379    </intensity-formula>
1380  </raw-data-type>
1381 
1382  <raw-data-type
1383    id="chipskipper"
1384    channels="2"
1385    name="ChipSkipper"
1386    table="RawDataChipSkipper"
1387    >
1388    <property
1389      name="Line_Counter"
1390      title="Line counter"
1391      description="Line counter."
1392      column="line_counter"
1393      type="int"
1394      averagemethod="none"
1395    />
1396    <property
1397      name="Flags"
1398      title="Flags"
1399      description="Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad."
1400      column="flags"
1401      type="string"
1402      averagemethod="none"
1403    />
1404    <property
1405      name="GS_Flags"
1406      title="GS flags"
1407      description="P = pass or M = marginal flag."
1408      column="gs_flags"
1409      type="string"
1410      averagemethod="none"
1411    />
1412    <property
1413      name="Cy3_Volume"
1414      title="Cy3 volume"
1415      description="Total integrated signal intensity in color channel Cy3."
1416      column="cy3_volume"
1417      channel="1"
1418      type="int"
1419      averagemethod="arithmetic_mean"
1420    />
1421    <property
1422      name="Cy3_AvVolpixel"
1423      title="Cy3 average intensity"
1424      description="Average intensity per pixel in color channel Cy3."
1425      column="cy3_avg"
1426      channel="1"
1427      type="float"
1428      averagemethod="arithmetic_mean"
1429    />
1430    <property
1431      name="Cy3_BGArith"
1432      title="Cy3 background (arithmetic)"
1433      description="Arithmetic average for local background in color channel Cy3."
1434      column="cy3_bg_arith"
1435      channel="1"
1436      type="float"
1437      averagemethod="arithmetic_mean"
1438    />
1439    <property
1440      name="Cy3_BGGeom"
1441      title="Cy3 background (geometric)"
1442      description="Geometric average for local background in color channel Cy3."
1443      column="cy3_bg_geom"
1444      channel="1"
1445      type="float"
1446      averagemethod="geometric_mean"
1447    />
1448    <property
1449      name="Cy3_BGMedian"
1450      title="Cy3 background (median)"
1451      description="Median average for local background in color channel Cy3."
1452      column="cy3_bg_median"
1453      channel="1"
1454      type="float"
1455      averagemethod="arithmetic_mean"
1456    />
1457    <property
1458      name="Cy3_BG_Tot"
1459      title="Cy3 background (total)"
1460      description="Total integrated background in color channel Cy3."
1461      column="cy3_bg_total"
1462      channel="1"
1463      type="float"
1464      averagemethod="arithmetic_mean"
1465    />
1466    <property
1467      name="Cy3_VolBG"
1468      title="Cy3 reduced intensity"
1469      description="Background reduced intensity of colour channel Cy3."
1470      column="cy3_reduced"
1471      channel="1"
1472      type="float"
1473      averagemethod="arithmetic_mean"
1474    />
1475    <property
1476      name="Cy3_Spotarea"
1477      title="Cy3 spot area"
1478      description="Area of spot in colour channel Cy3 in pixels."
1479      column="cy3_area"
1480      channel="1"
1481      type="float"
1482      averagemethod="arithmetic_mean"
1483    />
1484    <property
1485      name="Cy3_Satpixel"
1486      title="Cy3 saturated pixels"
1487      description="Number of saturated pixel in color channel Cy3."
1488      column="cy3_saturated"
1489      channel="1"
1490      type="float"
1491      averagemethod="arithmetic_mean"
1492    />
1493    <property
1494      name="Cy5_Volume"
1495      title="Cy5 volume"
1496      description="Total integrated signal intensity in color channel Cy5."
1497      column="cy5_volume"
1498      channel="2"
1499      type="int"
1500      averagemethod="arithmetic_mean"
1501    />
1502    <property
1503      name="Cy5_AvVolpixel"
1504      title="Cy5 average intensity"
1505      description="Average intensity per pixel in color channel Cy5."
1506      column="cy5_avg"
1507      channel="2"
1508      type="float"
1509      averagemethod="arithmetic_mean"
1510    />
1511    <property
1512      name="Cy5_BGArith"
1513      title="Cy5 background (arithmetic)"
1514      description="Arithmetic average for local background in color channel Cy5."
1515      column="cy5_bg_arith"
1516      channel="2"
1517      type="float"
1518      averagemethod="arithmetic_mean"
1519    />
1520    <property
1521      name="Cy5_BGGeom"
1522      title="Cy5 background (geometric)"
1523      description="Geometric average for local background in color channel Cy5."
1524      column="cy5_bg_geom"
1525      channel="2"
1526      type="float"
1527      averagemethod="geometric_mean"
1528    />
1529    <property
1530      name="Cy5_BGMedian"
1531      title="Cy5 background (median)"
1532      description="Median average for local background in color channel Cy5."
1533      column="cy5_bg_median"
1534      channel="2"
1535      type="float"
1536      averagemethod="arithmetic_mean"
1537    />
1538    <property
1539      name="Cy5_BG_Tot"
1540      title="Cy5 background (total)"
1541      description="Total integrated background in color channel Cy5."
1542      column="cy5_bg_total"
1543      channel="2"
1544      type="float"
1545      averagemethod="arithmetic_mean"
1546    />
1547    <property
1548      name="Cy5_VolBG"
1549      title="Cy5 reduced intensity"
1550      description="Background reduced intensity of colour channel Cy5."
1551      column="cy5_reduced"
1552      channel="2"
1553      type="float"
1554      averagemethod="arithmetic_mean"
1555    />
1556    <property
1557      name="Cy5_Spotarea"
1558      title="Cy5 spot area"
1559      description="Area of spot in colour channel Cy5 in pixels."
1560      column="cy5_area"
1561      channel="2"
1562      type="float"
1563      averagemethod="arithmetic_mean"
1564    />
1565    <property
1566      name="Cy5_Satpixel"
1567      title="Cy5 saturated pixels"
1568      description="Number of saturated pixel in color channel Cy5."
1569      column="cy5_saturated"
1570      channel="2"
1571      type="float"
1572      averagemethod="arithmetic_mean"
1573    />
1574    <property
1575      name="Rep_vol_BG2"
1576      title="Background reduced volume"
1577      description="Average of background reduced volume for onchip replicas (when calculated)."
1578      column="rep_vol"
1579      type="float"
1580      averagemethod="arithmetic_mean"
1581    />
1582    <property
1583      name="RatioCy5Cy3"
1584      title="Direct ratio"
1585      description="Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )."
1586      column="ratio"
1587      type="float"
1588      averagemethod="geometric_mean"
1589    />
1590    <property
1591      name="Directional_RatioCy5Cy3"
1592      title="Directional ratio"
1593      description="Directional ratio: if Ratio &gt; 1 then Directional = Ratio, if Ratio &gt; 1 then Directional = -1/Ratio."
1594      column="directional_ratio"
1595      type="float"
1596      averagemethod="geometric_mean"
1597    />
1598    <property
1599      name="Log2_RatioCy5Cy3"
1600      title="Log2 ratio"
1601      description="Log2 ratio: log2 (Ratio-Cy5/Cy3)"
1602      column="log2_ratio"
1603      type="float"
1604      averagemethod="arithmetic_mean"
1605    />
1606    <property
1607      name="Comp_ChannelCy3"
1608      title="Cy53 normalised intensity"
1609      description="Normalised intensity of Cy3_Vol-BG."
1610      column="cy3_normalised"
1611      channel="1"
1612      type="float"
1613      averagemethod="arithmetic_mean"
1614    />
1615    <property
1616      name="Comp_ChannelCy5"
1617      title="Cy5 normalised intensity"
1618      description="Normalised intensity of Cy5_Vol-BG."
1619      column="cy5_normalised"
1620      channel="2"
1621      type="float"
1622      averagemethod="arithmetic_mean"
1623    />
1624    <property
1625      name="Comp_RatioCy5Cy3"
1626      title="Compensated ratio"
1627      description="Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 )."
1628      column="compensated_ratio"
1629      type="float"
1630      averagemethod="geometric_mean"
1631    />
1632    <property
1633      name="Comp_Directional_RatioCy5Cy3"
1634      title="Compensated directional ratio"
1635      description="Compensated directional ratio: if Comp_Ratio &gt; 1 then Directional = Ratio, if Ratio &lt; 1 then Directional = -1/Ratio."
1636      column="comp_dir_ratio"
1637      type="float"
1638      averagemethod="geometric_mean"
1639    />
1640    <property
1641      name="Comp_Log2_Ratio"
1642      title="Compensated log2 ratio"
1643      description="Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3)."
1644      column="comp_log2_ratio"
1645      type="float"
1646      averagemethod="arithmetic_mean"
1647    />
1648    <property
1649      name="Comment"
1650      title="Comment"
1651      description="Additional description of spot."
1652      column="comment"
1653      type="string"
1654      averagemethod="none"
1655    />
1656    <property
1657      name="SNRtot"
1658      title="Squared average SNR"
1659      description="Squared average of Cy5_SNR and Cy3_SNR."
1660      column="snr_tot"
1661      type="float"
1662      averagemethod="geometric_mean"
1663    />
1664    <property
1665      name="SNRtot_Score"
1666      title="Squared average score SNR"
1667      description="Squared average of Cy5_%SNR and Cy3_%SNR."
1668      column="snr_tot_score"
1669      type="float"
1670      averagemethod="geometric_mean"
1671    />
1672    <property
1673      name="SNRGS"
1674      title="Saturated pixel"
1675      description="Number of saturated pixel in both colors (logical or)."
1676      column="sat_pixels"
1677      type="float"
1678      averagemethod="arithmetic_mean"
1679    />
1680    <property
1681      name="Replicas"
1682      title="Replicas"
1683      description="Replicas"
1684      column="replicas"
1685      type="float"
1686      averagemethod="none"
1687    />
1688    <property
1689      name="Regulation"
1690      title="Regulation"
1691      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."
1692      column="regulation"
1693      type="string"
1694      averagemethod="none"
1695    />
1696    <property
1697      name="GroupName"
1698      title="Group name"
1699      description="Group name for this spot."
1700      column="group_name"
1701      type="string"
1702      averagemethod="none"
1703    />
1704    <property
1705      name="MedianRatios"
1706      title="Median of ratios"
1707      description="Median of ratios (Cy5/Cy3) from all pixel in this spot."
1708      column="median_ratios"
1709      type="float"
1710      averagemethod="geometric_mean"
1711    />
1712    <property
1713      name="MedianRatiosSDev"
1714      title="Median of ratios (sdev%)"
1715      description="Standard deviation of Median of ratios in percent."
1716      column="median_ratios_sdev"
1717      type="float"
1718      averagemethod="arithmetic_mean"
1719    />
1720    <property
1721      name="RatioMedians"
1722      title="Ratio of medians"
1723      description="Ratio of Medians (Cy5/Cy3) from all pixel in this spot."
1724      column="ratio_medians"
1725      type="float"
1726      averagemethod="geometric_mean"
1727    />
1728    <property
1729      name="RatioMediansSDev"
1730      title="Ratio of medians (sdev%)"
1731      description="Standard deviation of Ratio of medians in percent."
1732      column="ratio_medians_sdev"
1733      type="float"
1734      averagemethod="arithmetic_mean"
1735    />
1736    <intensity-formula
1737      name="Volume"
1738      title="Volume"
1739      description="Total integrated signal intensity"
1740      >
1741      <formula 
1742        channel="1"
1743        expression="raw('Cy3_Volume')"
1744      />
1745      <formula 
1746        channel="2"
1747        expression="raw('Cy5_Volume')"
1748      />
1749    </intensity-formula>
1750    <intensity-formula
1751      name="VolBG"
1752      title="Reduced intensity"
1753      description="Background reduced intensity"
1754      >
1755      <formula 
1756        channel="1"
1757        expression="raw('Cy3_VolBG')"
1758      />
1759      <formula 
1760        channel="2"
1761        expression="raw('Cy5_VolBG')"
1762      />
1763    </intensity-formula>
1764  </raw-data-type>
1765
1766  <raw-data-type
1767    id="genetac"
1768    channels="2"
1769    name="GeneTAC"
1770    table="RawDataGeneTac"
1771    >
1772    <property
1773      name="medCy3"
1774      title="Signal median Cy3"
1775      description="Median of Cy3 signal intensity."
1776      column="med_cy3"
1777      channel="1"
1778      type="float"
1779      averagemethod="arithmetic_mean"
1780    />
1781    <property
1782      name="medCy5"
1783      title="Signal median Cy5"
1784      description="Median of Cy5 signal intensity."
1785      column="med_cy5"
1786      channel="2"
1787      type="float"
1788      averagemethod="arithmetic_mean"
1789    />
1790    <property
1791      name="medRatio"
1792      title="Signal median ratio"
1793      description="Ratio of median signal."
1794      column="med_ratio"
1795      type="float"
1796      averagemethod="geometric_mean"
1797    />
1798    <property
1799      name="bgCy3"
1800      title="Background median Cy3"
1801      description="Median of background intensity for Cy3."
1802      column="bg_cy3"
1803      channel="1"
1804      type="float"
1805      averagemethod="arithmetic_mean"
1806    />
1807    <property
1808      name="bgCy5"
1809      title="Background median Cy5"
1810      description="Median of background intensity for Cy5."
1811      column="bg_cy5"
1812      channel="2"
1813      type="float"
1814      averagemethod="arithmetic_mean"
1815    />
1816    <property
1817      name="bgRatio"
1818      title="Signal med ratio"
1819      description="Ratio of median background."
1820      column="bg_ratio"
1821      type="float"
1822      averagemethod="geometric_mean"
1823    />
1824    <intensity-formula
1825      name="medianfg"
1826      title="Median FG"
1827      description="Median foreground"
1828      >
1829      <formula 
1830        channel="1"
1831        expression="raw('medCy3')"
1832      />
1833      <formula 
1834        channel="2"
1835        expression="raw('medCy5')"
1836      />
1837    </intensity-formula>
1838    <intensity-formula
1839      name="median"
1840      title="Median FG - Median BG"
1841      description="Subtract median background from median foreground"
1842      >
1843      <formula 
1844        channel="1"
1845        expression="raw('medCy3') - raw('bgCy3')"
1846      />
1847      <formula 
1848        channel="2"
1849        expression="raw('medCy5') - raw('bgCy5')"
1850      />
1851    </intensity-formula>
1852  </raw-data-type>
1853 
1854  <raw-data-type
1855    id="imagene"
1856    channels="2"
1857    name="ImaGene"
1858    table="RawDataImaGene"
1859    >
1860    <property
1861      name="Field"
1862      title="Field"
1863      description="Name of a field where the spot is located."
1864      column="field"
1865      type="string"
1866      averagemethod="none"
1867    />
1868    <property
1869      name="Flag_Cy3"
1870      title="Flag cy3"
1871      description="Numeric code for the spot (0 - no flag, flag codes 1,...,7)."
1872      column="cy3_flag"
1873      channel="1"
1874      type="int"
1875      averagemethod="none"
1876    />
1877    <property
1878      name="SignalMean_Cy3"
1879      title="Mean signal cy3"
1880      description="Pixel intensity averaged over the local signal region."
1881      column="cy3_mean_signal"
1882      channel="1"
1883      type="float"
1884    />
1885    <property
1886      name="BackgroundMean_Cy3"
1887      title="Mean background cy3"
1888      description="Pixel intensity averaged over the local background region."
1889      column="cy3_mean_bg"
1890      channel="1"
1891      type="float"
1892      averagemethod="arithmetic_mean"
1893    />
1894    <property
1895      name="SignalMedian_Cy3"
1896      title="Median signal cy3"
1897      description="Median pixel intensity computed over the local signal region."
1898      column="cy3_median_signal"
1899      channel="1"
1900      type="float"
1901      averagemethod="arithmetic_mean"
1902    />
1903    <property
1904      name="BackgroundMedian_Cy3"
1905      title="Median background cy3"
1906      description="Median pixel intensity averaged over the local background region."
1907      column="cy3_median_bg"
1908      channel="1"
1909      type="float"
1910      averagemethod="arithmetic_mean"
1911    />
1912    <property
1913      name="SignalMode_Cy3"
1914      title="Mode signal cy3"
1915      description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
1916      column="cy3_mode_signal"
1917      channel="1"
1918      type="float"
1919      averagemethod="arithmetic_mean"
1920    />
1921    <property
1922      name="BackgroundMode_Cy3"
1923      title="Mode background cy3"
1924      description="Mode pixel intensity computed over the local background region."
1925      column="cy3_mode_bg"
1926      channel="1"
1927      type="float"
1928      averagemethod="arithmetic_mean"
1929    />
1930    <property
1931      name="SignalArea_Cy3"
1932      title="Signal area cy3"
1933      description="Number of pixels in the local signal region."
1934      column="cy3_area_signal"
1935      channel="1"
1936      type="int"
1937      averagemethod="arithmetic_mean"
1938    />
1939    <property
1940      name="BackgroundArea_Cy3"
1941      title="Background area cy3"
1942      description="Number of pixels in the local background region."
1943      column="cy3_area_bg"
1944      channel="1"
1945      type="int"
1946      averagemethod="arithmetic_mean"
1947    />
1948    <property
1949      name="SignalTotal_Cy3"
1950      title="Total signal cy3"
1951      description="Total pixel intensity summed over the local signal region."
1952      column="cy3_total_signal"
1953      channel="1"
1954      type="int"
1955      averagemethod="arithmetic_mean"
1956    />
1957    <property
1958      name="BackgroundTotal_Cy3"
1959      title="Total background cy3"
1960      description="Total pixel intensity summed over the local background region."
1961      column="cy3_total_bg"
1962      channel="1"
1963      type="int"
1964      averagemethod="arithmetic_mean"
1965    />
1966    <property
1967      name="ShapeRegularity_Cy3"
1968      title="Shape regularity cy3"
1969      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."
1970      column="cy3_shape"
1971      channel="1"
1972      type="float"
1973      averagemethod="geometric_mean"
1974    />
1975    <property
1976      name="IgnoredArea_Cy3"
1977      title="Ignored area cy3"
1978      description="Area of ignored regions directly neighboring (touching) the signal area is computed."
1979      column="cy3_area_ignored"
1980      channel="1"
1981      type="int"
1982      averagemethod="arithmetic_mean"
1983    />
1984    <property
1985      name="SpotArea_Cy3"
1986      title="Spot area cy3"
1987      description="Signal Area plus Ignored Area."
1988      column="cy3_area_spot"
1989      channel="1"
1990      type="int"
1991      averagemethod="arithmetic_mean"
1992    />
1993    <property
1994      name="IgnoredMedian_Cy3"
1995      title="Median ignored cy3"
1996      description="Median pixel intensity computed over the local ignored region."
1997      column="cy3_median_ignored"
1998      channel="1"
1999      type="float"
2000      averagemethod="arithmetic_mean"
2001    />
2002    <property
2003      name="AreaToPerimeter_Cy3"
2004      title="Area to perimeter cy3"
2005      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)."
2006      column="cy3_area_perimeter"
2007      channel="1"
2008      type="float"
2009      averagemethod="arithmetic_mean"
2010    />
2011    <property
2012      name="OpenPerimeter_Cy3"
2013      title="Open perimeter cy3"
2014      description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2015      column="cy3_open_perimeter"
2016      channel="1"
2017      type="float"
2018      averagemethod="arithmetic_mean"
2019    />
2020    <property
2021      name="XCoord_Cy3"
2022      title="X coordinate cy3"
2023      description="X coordinate (in pixels) of grid circle corresponding to the spot."
2024      column="cy3_x"
2025      channel="1"
2026      type="float"
2027      averagemethod="none"
2028    />
2029    <property
2030      name="YCoord_Cy3"
2031      title="Y coordinate cy3"
2032      description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2033      column="cy3_y"
2034      channel="1"
2035      type="float"
2036      averagemethod="none"
2037    />
2038    <property
2039      name="Diameter_Cy3"
2040      title="Diameter cy3"
2041      description="Diameter (in pixels) of grid circle corresponding to the spot."
2042      column="cy3_diameter"
2043      channel="1"
2044      type="int"
2045      averagemethod="arithmetic_mean"
2046    />
2047    <property
2048      name="PositionOffset_Cy3"
2049      title="Position offset cy3"
2050      description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2051      column="cy3_offset"
2052      channel="1"
2053      type="float"
2054      averagemethod="none"
2055    />
2056    <property
2057      name="OffsetX_Cy3"
2058      title="X offset cy3"
2059      description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2060      column="cy3_offset_x"
2061      channel="1"
2062      type="float"
2063      averagemethod="none"
2064    />
2065    <property
2066      name="OffsetY_Cy3"
2067      title="Y offset cy3"
2068      description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2069      column="cy3_offset_y"
2070      channel="1"
2071      type="float"
2072      averagemethod="none"
2073    />
2074    <property
2075      name="ExpectedX_Cy3"
2076      title="X expected cy3"
2077      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."
2078      column="cy3_x_expected"
2079      channel="1"
2080      type="float"
2081      averagemethod="none"
2082    />
2083    <property
2084      name="ExpectedY_Cy3"
2085      title="Y expected cy3"
2086      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."
2087      column="cy3_y_expected"
2088      channel="1"
2089      type="float"
2090      averagemethod="none"
2091    />
2092    <property
2093      name="CMX_Cy3"
2094      title="CM X coordinate cy3"
2095      description="X coordinate of the center of the mass of spot's signal region."
2096      column="cy3_x_cm"
2097      channel="1"
2098      type="float"
2099      averagemethod="none"
2100    />
2101    <property
2102      name="CMY_Cy3"
2103      title="CM Y coordinate cy3"
2104      description="Y coordinate of the center of the mass of spot's signal region."
2105      column="cy3_y_cm"
2106      channel="1"
2107      type="float"
2108      averagemethod="none"
2109    />
2110    <property
2111      name="CMOffset_Cy3"
2112      title="CM offset cy3"
2113      description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2114      column="cy3_offset_cm"
2115      channel="1"
2116      type="float"
2117      averagemethod="none"
2118    />
2119    <property
2120      name="CMOffsetX_Cy3"
2121      title="CM X offset cy3"
2122      description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2123      column="cy3_offset_x_cm"
2124      channel="1"
2125      type="float"
2126      averagemethod="none"
2127    />
2128    <property
2129      name="CMOffsetY_Cy3"
2130      title="CM Y offset cy3"
2131      description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2132      column="cy3_offset_y_cm"
2133      channel="1"
2134      type="float"
2135      averagemethod="none"
2136    />
2137    <property
2138      name="MinDiam_Cy3"
2139      title="Min diameter cy3"
2140      description="Diameter of the circle inscribed into the spot's signal region."
2141      column="cy3_diameter_min"
2142      channel="1"
2143      type="float"
2144      averagemethod="arithmetic_mean"
2145    />
2146    <property
2147      name="MaxDiam_Cy3"
2148      title="Max diameter cy3"
2149      description="Diameter of the circle, the spot's signal region can be inscribed in."
2150      column="cy3_diameter_max"
2151      channel="1"
2152      type="float"
2153      averagemethod="arithmetic_mean"
2154    />
2155    <property
2156      name="Control_Cy3"
2157      title="Control cy3"
2158      description="Name of a control type for current spot (no name means the spot is not a control spot)."
2159      column="cy3_control"
2160      channel="1"
2161      type="string"
2162      averagemethod="none"
2163    />
2164    <property
2165      name="FailedControl_Cy3"
2166      title="Failed control cy3"
2167      description="0 if the control passed all tests, 1 if at least one of the tests failed."
2168      column="cy3_control_failed"
2169      channel="1"
2170      type="boolean"
2171      averagemethod="none"
2172    />
2173    <property
2174      name="BackgroundContaminationPresent_Cy3"
2175      title="Bg contamination cy3"
2176      description="0 if the spot passed background contamination test, 1 if it did not."
2177      column="cy3_bg_contamination"
2178      channel="1"
2179      type="boolean"
2180      averagemethod="none"
2181    />
2182    <property
2183      name="SignalContaminationPresent_Cy3"
2184      title="Signal contamination cy3"
2185      description="0 if the spot passed signal contamination test, 1 if it did not."
2186      column="cy3_signal_contamination"
2187      channel="1"
2188      type="boolean"
2189      averagemethod="none"
2190    />
2191    <property
2192      name="IgnoredFailed_Cy3"
2193      title="Ignored % failed cy3"
2194      description="0 if the spot passed ignored percentage test, 1 if it did not."
2195      column="cy3_ignored_failed"
2196      channel="1"
2197      type="boolean"
2198      averagemethod="none"
2199    />
2200    <property
2201      name="OpenPerimeterFailed_Cy3"
2202      title="Open perimeter failed cy3"
2203      description="0 if the spot passed open perimeter test, 1 if it did not."
2204      column="cy3_perimeter_failed"
2205      channel="1"
2206      type="boolean"
2207      averagemethod="none"
2208    />
2209    <property
2210      name="ShapeRegularityFailed_Cy3"
2211      title="Shape regularity failed cy3"
2212      description="0 if the spot passed shape regularity test, 1 if it did not."
2213      column="cy3_shape_failed"
2214      channel="1"
2215      type="boolean"
2216      averagemethod="none"
2217    />
2218    <property
2219      name="PerimToAreaFailed_Cy3"
2220      title="Perimeter to area failed cy3"
2221      description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2222      column="cy3_areapm_failed"
2223      channel="1"
2224      type="boolean"
2225      averagemethod="none"
2226    />
2227    <property
2228      name="OffsetFailed_Cy3"
2229      title="Offset failed cy3"
2230      description="0 if the spot passed offset test, 1 if it did not."
2231      column="cy3_offset_failed"
2232      channel="1"
2233      type="boolean"
2234      averagemethod="none"
2235    />
2236    <property
2237      name="EmptySpot_Cy3"
2238      title="Empty spot cy3"
2239      description="1 if the spot is empty, 0 if not."
2240      column="cy3_empty_spot"
2241      channel="1"
2242      type="boolean"
2243      averagemethod="none"
2244    />
2245    <property
2246      name="NegativeSpot_Cy3"
2247      title="Negative spot cy3"
2248      description="1 if the spot was qualified as negative, 0 if it was not."
2249      column="cy3_negative_spot"
2250      channel="1"
2251      type="boolean"
2252      averagemethod="none"
2253    />
2254    <property
2255      name="SelectedSpot_Cy3"
2256      title="Selected spot cy3"
2257      description="1 if the spot was selected in the software view at time of save, 0 if not."
2258      column="cy3_selected_spot"
2259      channel="1"
2260      type="boolean"
2261      averagemethod="none"
2262    />
2263    <property
2264      name="SaturatedSpot_Cy3"
2265      title="Saturated spot cy3"
2266      description="1 if the spot was qualified as saturated, 0 if it was not."
2267      column="cy3_saturated_spot"
2268      channel="1"
2269      type="boolean"
2270      averagemethod="none"
2271    />
2272    <property
2273      name="SignalMean_Cy5"
2274      title="Mean signal cy5"
2275      description="Pixel intensity averaged over the local signal region."
2276      column="cy5_mean_signal"
2277      channel="2"
2278      type="float"
2279      averagemethod="arithmetic_mean"
2280    />
2281    <property
2282      name="BackgroundMean_Cy5"
2283      title="Mean background cy5"
2284      description="Pixel intensity averaged over the local background region."
2285      column="cy5_mean_bg"
2286      channel="2"
2287      type="float"
2288      averagemethod="arithmetic_mean"
2289    />
2290    <property
2291      name="SignalMedian_Cy5"
2292      title="Median signal cy5"
2293      description="Median pixel intensity computed over the local signal region."
2294      column="cy5_median_signal"
2295      channel="2"
2296      type="float"
2297      averagemethod="arithmetic_mean"
2298    />
2299    <property
2300      name="BackgroundMedian_Cy5"
2301      title="Median background cy5"
2302      description="Median pixel intensity averaged over the local background region."
2303      column="cy5_median_bg"
2304      channel="2"
2305      type="float"
2306      averagemethod="arithmetic_mean"
2307    />
2308    <property
2309      name="SignalMode_Cy5"
2310      title="Mode signal cy5"
2311      description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
2312      column="cy5_mode_signal"
2313      channel="2"
2314      type="float"
2315      averagemethod="arithmetic_mean"
2316    />
2317    <property
2318      name="BackgroundMode_Cy5"
2319      title="Mode background cy5"
2320      description="Mode pixel intensity computed over the local background region."
2321      column="cy5_mode_bg"
2322      channel="2"
2323      type="float"
2324      averagemethod="arithmetic_mean"
2325    />
2326    <property
2327      name="SignalArea_Cy5"
2328      title="Signal area cy5"
2329      description="Number of pixels in the local signal region."
2330      column="cy5_area_signal"
2331      channel="2"
2332      type="int"
2333      averagemethod="arithmetic_mean"
2334    />
2335    <property
2336      name="BackgroundArea_Cy5"
2337      title="Background area cy5"
2338      description="Number of pixels in the local background region."
2339      column="cy5_area_bg"
2340      channel="2"
2341      type="int"
2342      averagemethod="arithmetic_mean"
2343    />
2344    <property
2345      name="SignalTotal_Cy5"
2346      title="Total signal cy5"
2347      description="Total pixel intensity summed over the local signal region."
2348      column="cy5_total_signal"
2349      channel="2"
2350      type="int"
2351      averagemethod="arithmetic_mean"
2352    />
2353    <property
2354      name="BackgroundTotal_Cy5"
2355      title="Total background cy5"
2356      description="Total pixel intensity summed over the local background region."
2357      column="cy5_total_bg"
2358      channel="2"
2359      type="int"
2360      averagemethod="arithmetic_mean"
2361    />
2362    <property
2363      name="ShapeRegularity_Cy5"
2364      title="Shape regularity cy5"
2365      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."
2366      column="cy5_shape"
2367      channel="2"
2368      type="float"
2369      averagemethod="arithmetic_mean"
2370    />
2371    <property
2372      name="IgnoredArea_Cy5"
2373      title="Ignored area cy5"
2374      description="Area of ignored regions directly neighboring (touching) the signal area is computed."
2375      column="cy5_area_ignored"
2376      channel="2"
2377      type="int"
2378      averagemethod="arithmetic_mean"
2379    />
2380    <property
2381      name="SpotArea_Cy5"
2382      title="Spot area cy5"
2383      description="Signal Area plus Ignored Area."
2384      column="cy5_area_spot"
2385      channel="2"
2386      type="int"
2387      averagemethod="arithmetic_mean"
2388    />
2389    <property
2390      name="IgnoredMedian_Cy5"
2391      title="Median ignored cy5"
2392      description="Median pixel intensity computed over the local ignored region."
2393      column="cy5_median_ignored"
2394      channel="2"
2395      type="float"
2396      averagemethod="arithmetic_mean"
2397    />
2398    <property
2399      name="AreaToPerimeter_Cy5"
2400      title="Area to perimeter cy5"
2401      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)."
2402      column="cy5_area_perimeter"
2403      channel="2"
2404      type="float"
2405      averagemethod="arithmetic_mean"
2406    />
2407    <property
2408      name="OpenPerimeter_Cy5"
2409      title="Open perimeter cy5"
2410      description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2411      column="cy5_open_perimeter"
2412      channel="2"
2413      type="float"
2414      averagemethod="arithmetic_mean"
2415    />
2416    <property
2417      name="XCoord_Cy5"
2418      title="X coordinate cy5"
2419      description="X coordinate (in pixels) of grid circle corresponding to the spot."
2420      column="cy5_x"
2421      channel="2"
2422      type="float"
2423      averagemethod="none"
2424    />
2425    <property
2426      name="YCoord_Cy5"
2427      title="Y coordinate cy5"
2428      description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2429      column="cy5_y"
2430      channel="2"
2431      type="float"
2432      averagemethod="none"
2433    />
2434    <property
2435      name="Diameter_Cy5"
2436      title="Diameter cy5"
2437      description="Diameter (in pixels) of grid circle corresponding to the spot."
2438      column="cy5_diameter"
2439      channel="2"
2440      type="int"
2441      averagemethod="arithmetic_mean"
2442    />
2443    <property
2444      name="PositionOffset_Cy5"
2445      title="Position offset cy5"
2446      description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2447      column="cy5_offset"
2448      channel="2"
2449      type="float"
2450      averagemethod="none"
2451    />
2452    <property
2453      name="OffsetX_Cy5"
2454      title="X offset cy5"
2455      description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2456      column="cy5_offset_x"
2457      channel="2"
2458      type="float"
2459      averagemethod="none"
2460    />
2461    <property
2462      name="OffsetY_Cy5"
2463      title="Y offset cy5"
2464      description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2465      column="cy5_offset_y"
2466      channel="2"
2467      type="float"
2468      averagemethod="none"
2469    />
2470    <property
2471      name="ExpectedX_Cy5"
2472      title="X expected cy5"
2473      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."
2474      column="cy5_x_expected"
2475      channel="2"
2476      type="float"
2477      averagemethod="none"
2478    />
2479    <property
2480      name="ExpectedY_Cy5"
2481      title="Y expected cy5"
2482      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."
2483      column="cy5_y_expected"
2484      channel="2"
2485      type="float"
2486      averagemethod="none"
2487    />
2488    <property
2489      name="CMX_Cy5"
2490      title="CM X coordinate cy5"
2491      description="X coordinate of the center of the mass of spot's signal region."
2492      column="cy5_x_cm"
2493      channel="2"
2494      type="float"
2495      averagemethod="none"
2496    />
2497    <property
2498      name="CMY_Cy5"
2499      title="CM Y coordinate cy5"
2500      description="Y coordinate of the center of the mass of spot's signal region."
2501      column="cy5_y_cm"
2502      channel="2"
2503      type="float"
2504      averagemethod="none"
2505    />
2506    <property
2507      name="CMOffset_Cy5"
2508      title="CM offset cy5"
2509      description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2510      column="cy5_offset_cm"
2511      channel="2"
2512      type="float"
2513      averagemethod="none"
2514    />
2515    <property
2516      name="CMOffsetX_Cy5"
2517      title="CM X offset cy5"
2518      description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2519      column="cy5_offset_x_cm"
2520      channel="2"
2521      type="float"
2522      averagemethod="none"
2523    />
2524    <property
2525      name="CMOffsetY_Cy5"
2526      title="CM Y offset cy5"
2527      description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2528      column="cy5_offset_y_cm"
2529      channel="2"
2530      type="float"
2531      averagemethod="none"
2532    />
2533    <property
2534      name="MinDiam_Cy5"
2535      title="Min diameter cy5"
2536      description="Diameter of the circle inscribed into the spot's signal region."
2537      column="cy5_diameter_min"
2538      channel="2"
2539      type="float"
2540      averagemethod="arithmetic_mean"
2541    />
2542    <property
2543      name="MaxDiam_Cy5"
2544      title="Max diameter cy5"
2545      description="Diameter of the circle, the spot's signal region can be inscribed in."
2546      column="cy5_diameter_max"
2547      channel="2"
2548      type="float"
2549      averagemethod="arithmetic_mean"
2550    />
2551    <property
2552      name="Control_Cy5"
2553      title="Control cy5"
2554      description="Name of a control type for current spot (no name means the spot is not a control spot)."
2555      column="cy5_control"
2556      channel="2"
2557      type="string"
2558      averagemethod="none"
2559    />
2560    <property
2561      name="FailedControl_Cy5"
2562      title="Failed control cy5"
2563      description="0 if the control passed all tests, 1 if at least one of the tests failed."
2564      column="cy5_control_failed"
2565      channel="2"
2566      type="boolean"
2567      averagemethod="none"
2568    />
2569    <property
2570      name="BackgroundContaminationPresent_Cy5"
2571      title="Bg contamination cy5"
2572      description="0 if the spot passed background contamination test, 1 if it did not."
2573      column="cy5_bg_contamination"
2574      channel="2"
2575      type="boolean"
2576      averagemethod="none"
2577    />
2578    <property
2579      name="SignalContaminationPresent_Cy5"
2580      title="Signal contamination cy5"
2581      description="0 if the spot passed signal contamination test, 1 if it did not."
2582      column="cy5_signal_contamination"
2583      channel="2"
2584      type="boolean"
2585      averagemethod="none"
2586    />
2587    <property
2588      name="IgnoredFailed_Cy5"
2589      title="Ignored % failed cy5"
2590      description="0 if the spot passed ignored percentage test, 1 if it did not."
2591      column="cy5_ignored_failed"
2592      channel="2"
2593      type="boolean"
2594      averagemethod="none"
2595    />
2596    <property
2597      name="OpenPerimeterFailed_Cy5"
2598      title="Open perimeter failed cy5"
2599      description="0 if the spot passed open perimeter test, 1 if it did not."
2600      column="cy5_perimeter_failed"
2601      channel="2"
2602      type="boolean"
2603      averagemethod="none"
2604    />
2605    <property
2606      name="ShapeRegularityFailed_Cy5"
2607      title="Shape regularity failed cy5"
2608      description="0 if the spot passed shape regularity test, 1 if it did not."
2609      column="cy5_shape_failed"
2610      channel="2"
2611      type="boolean"
2612      averagemethod="none"
2613    />
2614    <property
2615      name="PerimToAreaFailed_Cy5"
2616      title="Perimeter to area failed cy5"
2617      description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2618      column="cy5_areapm_failed"
2619      channel="2"
2620      type="boolean"
2621      averagemethod="none"
2622    />
2623    <property
2624      name="OffsetFailed_Cy5"
2625      title="Offset failed cy5"
2626      description="0 if the spot passed offset test, 1 if it did not."
2627      column="cy5_offset_failed"
2628      channel="2"
2629      type="boolean"
2630      averagemethod="none"
2631    />
2632    <property
2633      name="EmptySpot_Cy5"
2634      title="Empty spot cy5"
2635      description="1 if the spot is empty, 0 if not."
2636      column="cy5_empty_spot"
2637      channel="2"
2638      type="boolean"
2639      averagemethod="none"
2640    />
2641    <property
2642      name="NegativeSpot_Cy5"
2643      title="Negative spot cy5"
2644      description="1 if the spot was qualified as negative, 0 if it was not."
2645      column="cy5_negative_spot"
2646      channel="2"
2647      type="boolean"
2648      averagemethod="none"
2649    />
2650    <property
2651      name="SelectedSpot_Cy5"
2652      title="Selected spot cy5"
2653      description="1 if the spot was selected in the software view at time of save, 0 if not."
2654      column="cy5_selected_spot"
2655      channel="2"
2656      type="boolean"
2657      averagemethod="none"
2658    />
2659    <property
2660      name="SaturatedSpot_Cy5"
2661      title="Saturated spot cy5"
2662      description="1 if the spot was qualified as saturated, 0 if it was not."
2663      column="cy5_saturated_spot"
2664      channel="2"
2665      type="boolean"
2666      averagemethod="none"
2667    />
2668    <intensity-formula
2669      name="mean"
2670      title="Mean FG - Mean BG"
2671      description="Subtract mean background from mean foreground"
2672      >
2673      <formula 
2674        channel="1"
2675        expression="raw('SignalMean_Cy3') - raw('BackgroundMean_Cy3')"
2676      />
2677      <formula 
2678        channel="2"
2679        expression="raw('SignalMean_Cy5') - raw('BackgroundMean_Cy5')"
2680      />
2681    </intensity-formula>
2682    <intensity-formula
2683      name="median"
2684      title="Median FG - Median BG"
2685      description="Subtract meadian background from median foreground"
2686      >
2687      <formula 
2688        channel="1"
2689        expression="raw('SignalMedian_Cy3') - raw('BackgroundMedian_Cy3')"
2690      />
2691      <formula 
2692        channel="2"
2693        expression="raw('SignalMedian_Cy5') - raw('BackgroundMedian_Cy5')"
2694      />
2695    </intensity-formula>
2696    <intensity-formula
2697      name="medianmean"
2698      title="Median FG - Mean BG"
2699      description="Subtract mean background from median foreground"
2700      >
2701      <formula 
2702        channel="1"
2703        expression="raw('SignalMedian_Cy3') - raw('BackgroundMean_Cy3')"
2704      />
2705      <formula 
2706        channel="2"
2707        expression="raw('SignalMedian_Cy5') - raw('BackgroundMean_Cy5')"
2708      />
2709    </intensity-formula>
2710    <intensity-formula
2711      name="meanmedian"
2712      title="Mean FG - Median BG"
2713      description="Subtract median background from mean foreground"
2714      >
2715      <formula 
2716        channel="1"
2717        expression="raw('SignalMean_Cy3') - raw('BackgroundMedian_Cy3')"
2718      />
2719      <formula 
2720        channel="2"
2721        expression="raw('SignalMean_Cy5') - raw('BackgroundMedian_Cy5')"
2722      />
2723    </intensity-formula>
2724    <intensity-formula
2725      name="meanfg"
2726      title="Mean FG"
2727      description="Mean foreground"
2728      >
2729      <formula 
2730        channel="1"
2731        expression="raw('SignalMean_Cy3')"
2732      />
2733      <formula 
2734        channel="2"
2735        expression="raw('SignalMean_Cy5')"
2736      />
2737    </intensity-formula>
2738    <intensity-formula
2739      name="medianfg"
2740      title="Median FG"
2741      description="Median foreground"
2742      >
2743      <formula 
2744        channel="1"
2745        expression="raw('SignalMedian_Cy3')"
2746      />
2747      <formula 
2748        channel="2"
2749        expression="raw('SignalMedian_Cy5')"
2750      />
2751    </intensity-formula>
2752    <intensity-formula
2753      name="medianfgmeanmedianbg"
2754      title="Median FG - Mean(Median BG)"
2755      description="Subtract mean of median backgrounds from median foreground"
2756      >
2757      <formula 
2758        channel="1"
2759        expression="raw('SignalMedian_Cy3') - mean('BackgroundMedian_Cy3')"
2760      />
2761      <formula 
2762        channel="2"
2763        expression="raw('SignalMedian_Cy5') - mean('BackgroundMedian_Cy5')"
2764      />
2765    </intensity-formula>
2766    <intensity-formula
2767      name="meanfgmeanmeanbg"
2768      title="Mean FG - Mean(Mean BG)"
2769      description="Subtract mean of mean backgrounds from mean foreground"
2770      >
2771      <formula 
2772        channel="1"
2773        expression="raw('SignalMean_Cy3') - mean('BackgroundMean_Cy3')"
2774      />
2775      <formula 
2776        channel="2"
2777        expression="raw('SignalMean_Cy5') - mean('BackgroundMean_Cy5')"
2778      />
2779    </intensity-formula>
2780    <intensity-formula
2781      name="medianfgmeanmeanbg"
2782      title="Median FG - Mean(Mean BG)"
2783      description="Subtract mean of mean backgrounds from median foreground"
2784      >
2785      <formula 
2786        channel="1"
2787        expression="raw('SignalMedian_Cy3') - mean('BackgroundMean_Cy3')"
2788      />
2789      <formula 
2790        channel="2"
2791        expression="raw('SignalMedian_Cy5') - mean('BackgroundMean_Cy5')"
2792      />
2793    </intensity-formula>
2794    <intensity-formula
2795      name="meanfgmeanmedianbg"
2796      title="Mean FG - Mean(Median BG)"
2797      description="Subtract mean of median backgrounds from mean foreground"
2798      >
2799      <formula 
2800        channel="1"
2801        expression="raw('SignalMean_Cy3') - mean('BackgroundMedian_Cy3')"
2802      />
2803      <formula 
2804        channel="2"
2805        expression="raw('SignalMean_Cy5') - mean('BackgroundMedian_Cy5')"
2806      />
2807    </intensity-formula>
2808  </raw-data-type>
2809 
2810  <raw-data-type
2811    id="quantarraybiotin"
2812    channels="1"
2813    name="QuantArray Biotin"
2814    table="RawDataQuantArrayBiotin"
2815    >
2816    <property
2817      name="Number"
2818      title="Number"
2819      description="Number."
2820      column="number"
2821      type="int"
2822      averagemethod="none"
2823    />
2824    <property
2825      name="BiotinIntensity"
2826      title="Intensity"
2827      description="Mean pixel biotin foreground intensity in biotin channel."
2828      column="intensity"
2829      channel="1"
2830      type="float"
2831      averagemethod="arithmetic_mean"
2832    />
2833    <property
2834      name="BiotinBackground"
2835      title="Background"
2836      description="Mean pixel biotin background intensity in biotin channel."
2837      column="background"
2838      channel="1"
2839      type="float"
2840      averagemethod="arithmetic_mean"
2841    />
2842    <property
2843      name="BiotinDiameter"
2844      title="Diameter"
2845      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."
2846      column="diameter"
2847      channel="1"
2848      type="float"
2849      averagemethod="arithmetic_mean"
2850    />
2851    <property
2852      name="BiotinArea"
2853      title="Area"
2854      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."
2855      column="area"
2856      channel="1"
2857      type="int"
2858      averagemethod="arithmetic_mean"
2859    />
2860    <property
2861      name="BiotinFootprint"
2862      title="Footprint"
2863      description="The distance between the expected position of a spot and its actual measured position (in microns)."
2864      column="footprint"
2865      channel="1"
2866      type="float"
2867      averagemethod="none"
2868    />
2869    <property
2870      name="BiotinCircularity"
2871      title="Circularity"
2872      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."
2873      column="cirularity"
2874      channel="1"
2875      type="float"
2876      averagemethod="none"
2877    />
2878    <property
2879      name="BiotinSpotUniformity"
2880      title="Spot uniformity"
2881      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."
2882      column="uniformity"
2883      channel="1"
2884      type="float"
2885      averagemethod="none"
2886    />
2887    <property
2888      name="BiotinBkgUniformity"
2889      title="Background uniformity"
2890      description="The uniformity of the pixels used in the background intensity calculation."
2891      column="bg_uniformity"
2892      channel="1"
2893      type="float"
2894      averagemethod="none"
2895    />
2896    <property
2897      name="BiotinSignalNoiseRatio"
2898      title="Signal noise ratio"
2899      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."
2900      column="snr"
2901      channel="1"
2902      type="float"
2903      averagemethod="geometric_mean"
2904    />
2905    <property
2906      name="BiotinConfidence"
2907      title="Confidence"
2908      description="Confidence."
2909      column="confidence"
2910      channel="1"
2911      type="int"
2912      averagemethod="none"
2913    />
2914    <property
2915      name="IgnoreFilter"
2916      title="Ignore filter"
2917      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2918      column="ignore_filter"
2919      type="int"
2920      averagemethod="none"
2921    />
2922    <property
2923      name="BiotinRatio"
2924      title="Ratio"
2925      description="The portion of the overall spot fluorescence contributed by biotin channel (normalized so that biotin channel contribution equals 1)."
2926      column="ratio"
2927      channel="1"
2928      type="int"
2929      averagemethod="geometric_mean"
2930    />
2931    <property
2932      name="BiotinPercent"
2933      title="Percent"
2934      description="The portion of the overall spot fluorescence contributed by biotin channel (in percent)."
2935      column="precent"
2936      channel="1"
2937      type="float"
2938      averagemethod="arithmetic_mean"
2939    />
2940    <property
2941      name="BiotinDiameterFilter"
2942      title="Diameter filter"
2943      description="Biotin diameter filter."
2944      column="diameter_filter"
2945      type="int"
2946      averagemethod="none"
2947    />
2948    <property
2949      name="BiotinAreaFilter"
2950      title="Area filter"
2951      description="Biotin area filter."
2952      column="area_filter"
2953      type="int"
2954      averagemethod="none"
2955    />
2956    <property
2957      name="BiotinFootprintFilter"
2958      title="Footprint filter"
2959      description="Biotin footprint filter."
2960      column="footprint_filter"
2961      type="int"
2962      averagemethod="none"
2963    />
2964    <property
2965      name="BiotinCircularityFilter"
2966      title="Circularity filter"
2967      description="Biotin circularity filter."
2968      column="circularity_filter"
2969      type="int"
2970      averagemethod="none"
2971    />
2972    <property
2973      name="BiotinSpotUniformityFilter"
2974      title="Spot uniformity filter"
2975      description="Biotin spot uniformity filter."
2976      column="uniformity_filter"
2977      type="int"
2978      averagemethod="none"
2979    />
2980    <property
2981      name="BiotinBkgUniformityFilter"
2982      title="Background uniformity filter"
2983      description="Biotin background uniformity filter."
2984      column="bg_uniformity_filter"
2985      type="int"
2986      averagemethod="none"
2987    />
2988    <property
2989      name="BiotinSignalNoiseRatioFilter"
2990      title="Signal noise ratio filter"
2991      description="Biotin signal noise ratio filter."
2992      column="snr_filter"
2993      type="int"
2994    />
2995    <property
2996      name="BiotinReplicateFilter"
2997      title="Replicate filter"
2998      description="Biotin replicate filter."
2999      column="replicate_filter"
3000      type="int"
3001      averagemethod="none"
3002    />
3003    <intensity-formula
3004      name="meanfg"
3005      title="Mean FG"
3006      description="Mean foreground intensity"
3007      >
3008      <formula 
3009        channel="1"
3010        expression="raw('intensity')"
3011      />
3012    </intensity-formula>
3013    <intensity-formula
3014      name="mean"
3015      title="Mean FG - Mean BG"
3016      description="Subtract mean background from mean foreground"
3017      >
3018      <formula 
3019        channel="1"
3020        expression="raw('BiotinIntensity') - raw('BiotinBackground')"
3021      />
3022    </intensity-formula>
3023  </raw-data-type>
3024 
3025  <raw-data-type
3026    id="quantarraycy"
3027    channels="2"
3028    name="QuantArray Cy"
3029    table="RawDataQuantArrayCy"
3030    >
3031    <property
3032      name="Cy3Intensity"
3033      title="Mean Cy3 intensity"
3034      description="Mean pixel Cy3 foreground intensity in Channel Cy3."
3035      column="cy3_mean"
3036      channel="1"
3037      type="float"
3038      averagemethod="arithmetic_mean"
3039    />
3040    <property
3041      name="Cy3Background"
3042      title="Mean Cy3 background"
3043      description="Mean pixel Cy3 background intensity in Channel Cy3."
3044      column="cy3_mean_bg"
3045      channel="1"
3046      type="float"
3047      averagemethod="arithmetic_mean"
3048    />
3049    <property
3050      name="Cy3Diameter"
3051      title="Cy3 spot diameter"
3052      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."
3053      column="cy3_diameter"
3054      channel="1"
3055      type="float"
3056      averagemethod="arithmetic_mean"
3057    />
3058    <property
3059      name="Cy3Area"
3060      title="Cy3 spot area"
3061      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."
3062      column="cy3_area"
3063      channel="1"
3064      type="int"
3065      averagemethod="arithmetic_mean"
3066    />
3067    <property
3068      name="Cy3Footprint"
3069      title="Cy3 footprint"
3070      description="The distance between the expected position of a spot and its actual measured position (in microns)."
3071      column="cy3_footprint"
3072      channel="1"
3073      type="float"
3074      averagemethod="none"
3075    />
3076    <property
3077      name="Cy3Circularity"
3078      title="Cy3 circularity"
3079      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."
3080      column="cy3_circularity"
3081      channel="1"
3082      type="float"
3083      averagemethod="none"
3084    />
3085    <property
3086      name="Cy3SpotUniformity"
3087      title="Cy3 spot uniformity"
3088      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."
3089      column="cy3_uniformity"
3090      channel="1"
3091      type="float"
3092      averagemethod="none"
3093    />
3094    <property
3095      name="Cy3BkgUniformity"
3096      title="Cy3 background uniformity"
3097      description="The uniformity of the pixels used in the background intensity calculation."
3098      column="cy3_bg_uniformity"
3099      channel="1"
3100      type="float"
3101      averagemethod="none"
3102    />
3103    <property
3104      name="Cy3SignalNoiseRatio"
3105      title="Cy3 signal noise ratio"
3106      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."
3107      column="cy3_snr"
3108      channel="1"
3109      type="float"
3110      averagemethod="geometric_mean"
3111    />
3112    <property
3113      name="Cy3Confidence"
3114      title="Cy3 confidence"
3115      description="Unused QuantArray feature, will always = 1."
3116      column="cy3_confidence"
3117      channel="2"
3118      type="int"
3119      averagemethod="none"
3120    />
3121    <property
3122      name="Cy5Intensity"
3123      title="Mean Cy5 intensity"
3124      description="Mean pixel Cy5 foreground intensity in Channel Cy5."
3125      column="cy5_mean"
3126      channel="2"
3127      type="float"
3128      averagemethod="arithmetic_mean"
3129    />
3130    <property
3131      name="Cy5Background"
3132      title="Mean Cy5 background"
3133      description="Mean pixel Cy5 background intensity in Channel Cy5."
3134      column="cy5_mean_bg"
3135      channel="2"
3136      type="float"
3137      averagemethod="arithmetic_mean"
3138    />
3139    <property
3140      name="Cy5Diameter"
3141      title="Cy5 spot diameter"
3142      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."
3143      column="cy5_diameter"
3144      channel="2"
3145      type="float"
3146      averagemethod="arithmetic_mean"
3147    />
3148    <property
3149      name="Cy5Area"
3150      title="Cy5 spot area"
3151      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."
3152      column="cy5_area"
3153      channel="2"
3154      type="int"
3155      averagemethod="arithmetic_mean"
3156    />
3157    <property
3158      name="Cy5Footprint"
3159      title="Cy5 footprint"
3160      description="The distance between the expected position of a spot and its actual measured position (in microns)."
3161      column="cy5_footprint"
3162      channel="2"
3163      type="float"
3164      averagemethod="none"
3165    />
3166    <property
3167      name="Cy5Circularity"
3168      title="Cy5 circularity"
3169      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."
3170      column="cy5_circularity"
3171      channel="2"
3172      type="float"
3173      averagemethod="none"
3174    />
3175    <property
3176      name="Cy5SpotUniformity"
3177      title="Cy5 spot uniformity"
3178      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."
3179      column="cy5_uniformity"
3180      channel="2"
3181      type="float"
3182      averagemethod="none"
3183    />
3184    <property
3185      name="Cy5BkgUniformity"
3186      title="Cy5 background uniformity"
3187      description="The uniformity of the pixels used in the background intensity calculation."
3188      column="cy5_bg_uniformity"
3189      channel="2"
3190      type="float"
3191      averagemethod="none"
3192    />
3193    <property
3194      name="Cy5SignalNoiseRatio"
3195      title="Cy5 signal noise ratio"
3196      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."
3197      column="cy5_snr"
3198      channel="2"
3199      type="float"
3200      averagemethod="geometric_mean"
3201    />
3202    <property
3203      name="Cy5Confidence"
3204      title="Cy5 confidence"
3205      description="Unused QuantArray feature, will always = 1."
3206      column="cy5_confidence"
3207      channel="2"
3208      type="int"
3209      averagemethod="none"
3210    />
3211    <property
3212      name="IgnoreFilter"
3213      title="Ignore filter"
3214      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
3215      column="ignore_filter"
3216      type="int"
3217      averagemethod="none"
3218    />
3219    <property
3220      name="Cy3Ratio"
3221      title="Cy3 ratio"
3222      description="The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1)."
3223      column="cy3_ratio"
3224      channel="1"
3225      type="float"
3226      averagemethod="geometric_mean"
3227    />
3228    <property
3229      name="Cy3Percent"
3230      title="Cy3 precent"
3231      description="The portion of the overall spot fluorescence contributed by channel Cy3 (in percent)."
3232      column="cy3_percent"
3233      channel="1"
3234      type="float"
3235    />
3236    <property
3237      name="Cy3SignalNoiseRatioFilter"
3238      title="Cy3 signal noise ratio filter"
3239      description="Cy3 signal noise ratio filter"
3240      column="cy3_snr_filter"
3241      channel="1"
3242      type="float"
3243      averagemethod="none"
3244    />
3245    <property
3246      name="Cy5Ratio"
3247      title="Cy5 ratio"
3248      description="The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1)."
3249      column="cy5_ratio"
3250      channel="2"
3251      type="float"
3252      averagemethod="geometric_mean"
3253    />
3254    <property
3255      name="Cy5Percent"
3256      title="Cy5 precent"
3257      description="The portion of the overall spot fluorescence contributed by channel Cy5 (in percent)."
3258      column="cy5_percent"
3259      channel="2"
3260      type="float"
3261      averagemethod="arithmetic_mean"
3262    />
3263    <property
3264      name="Cy5SignalNoiseRatioFilter"
3265      title="Cy5 signal noise ratio filter"
3266      description="Cy5 signal noise ratio filter"
3267      column="cy5_snr_filter"
3268      channel="2"
3269      type="float"
3270      averagemethod="none"
3271    />
3272    <property
3273      name="log_normalised"
3274      title="Normalized ratio"
3275      description="Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1"
3276      column="log_normalised"
3277      type="float"
3278      averagemethod="arithmetic_mean"
3279    />
3280    <intensity-formula
3281      name="meanfg"
3282      title="Mean FG"
3283      description="Mean foreground intensity"
3284      >
3285      <formula 
3286        channel="1"
3287        expression="raw('Cy3Intensity')"
3288      />
3289      <formula 
3290        channel="2"
3291        expression="raw('Cy5Intensity')"
3292      />
3293    </intensity-formula>
3294    <intensity-formula
3295      name="mean"
3296      title="Mean FG - Mean BG"
3297      description="Subtract mean background from mean foreground"
3298      >
3299      <formula 
3300        channel="1"
3301        expression="raw('Cy3Intensity') - raw('Cy3Background')"
3302      />
3303      <formula 
3304        channel="2"
3305        expression="raw('Cy5Intensity') - raw('Cy5Background')"
3306      />
3307    </intensity-formula>
3308  </raw-data-type>
3309 
3310  <raw-data-type
3311    id="spotfinder"
3312    channels="2"
3313    name="Spotfinder"
3314    table="RawDataSpotfinder"
3315    >
3316    <property
3317      name="intA"
3318      title="Intensity A"
3319      description="Spot intensity in channel A corrected for background."
3320      column="int_a"
3321      type="int"
3322      channel="1"
3323      averagemethod="arithmetic_mean"
3324    />
3325    <property
3326      name="intB"
3327      title="Intensity B"
3328      description="Spot intensity in channel B corrected for background."
3329      column="int_b"
3330      type="int"
3331      channel="2"
3332      averagemethod="arithmetic_mean"
3333    />
3334    <property
3335      name="meanRatio"
3336      title="Mean ratio"
3337      description="Spot mean ratio."
3338      column="mean_ratio"
3339      type="float"
3340      averagemethod="geometric_mean"
3341    />
3342    <property
3343      name="area"
3344      title="Area"
3345      description="Spot total area in pixels."
3346      column="area"
3347      type="int"
3348      averagemethod="arithmetic_mean"
3349    />
3350    <property
3351      name="saturation"
3352      title="Saturation factor"
3353      description="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration."
3354      column="saturation"
3355      type="float"
3356      averagemethod="arithmetic_mean"
3357    />
3358    <property
3359      name="medianRatio"
3360      title="Median ratio"
3361      description="Spot median ratio."
3362      column="median_ratio"
3363      type="float"
3364      averagemethod="geometric_mean"
3365    />
3366    <property
3367      name="modeRatio"
3368      title="Mode ratio"
3369      description="Spot mode ratio."
3370      column="mode_ratio"
3371      type="float"
3372      averagemethod="geometric_mean"
3373    />
3374    <property
3375      name="bgA"
3376      title="Background A"
3377      description="Spot background in channel A."
3378      column="bg_a"
3379      channel="1"
3380      type="int"
3381      averagemethod="arithmetic_mean"
3382    />
3383    <property
3384      name="bgB"
3385      title="Background B"
3386      description="Spot background in channel B."
3387      column="bg_b"
3388      channel="2"
3389      type="int"
3390      averagemethod="arithmetic_mean"
3391    />
3392    <property
3393      name="flagA"
3394      title="Flag A"
3395      description="Spot flag in channel A. This flag is set by QC filter."
3396      column="flag_a"
3397      channel="1"
3398      type="string"
3399      averagemethod="none"
3400    />
3401    <property
3402      name="flagB"
3403      title="Flag B"
3404      description="Spot flag in channel B. This flag is set by QC filter."
3405      column="flag_b"
3406      channel="2"
3407      type="string"
3408      averagemethod="none"
3409    />
3410    <property
3411      name="qcA"
3412      title="Spot QC score A"
3413      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."
3414      column="qc_a"
3415      channel="1"
3416      type="float"
3417      averagemethod="none"
3418    />
3419    <property
3420      name="qcB"
3421      title="Spot QC score B"
3422      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."
3423      column="qc_b"
3424      channel="2"
3425      type="float"
3426      averagemethod="none"
3427    />
3428    <property
3429      name="qcTotal"
3430      title="Total QC"
3431      description="Spot total QC score. This is a mean of QC scores in channels A and B."
3432      column="qc_total"
3433      type="float"
3434      averagemethod="none"
3435    />
3436    <property
3437      name="flag"
3438      title="Flag"
3439      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."
3440      column="flag"
3441      type="string"
3442      averagemethod="none"
3443    />
3444    <intensity-formula
3445      name="int"
3446      title="Spot intensity"
3447      description="Spot intensity corrected for background."
3448      >
3449      <formula 
3450        channel="1"
3451        expression="raw('intA')"
3452      />
3453      <formula 
3454        channel="2"
3455        expression="raw('intB')"
3456      />
3457    </intensity-formula>
3458  </raw-data-type>
3459  <raw-data-type 
3460    id="illumina" 
3461    channels="1" 
3462    name="Illumina" 
3463    table="RawDataIllumina">
3464    <property
3465      name="MIN_Signal"
3466      title="MIN_Signal"
3467      description="Minimum intensity of the gene in the group."
3468      column="minSignal"
3469      type="float"
3470      averagemethod="arithmetic_mean"
3471    />
3472    <property
3473      name="AVG_Signal"
3474      title="AVG_Signal"
3475      description="Average intensity of the gene in the group."
3476      column="avgSignal"
3477      type="float"
3478      averagemethod="arithmetic_mean"
3479    />
3480    <property
3481      name="MAX_Signal"
3482      title="MAX_Signal"
3483      description="Maximum intensity of the gene in the group."
3484      column="maxSignal"
3485      type="float"
3486      averagemethod="arithmetic_mean" 
3487    />
3488    <property
3489      name="NARRAYS"
3490      title="NARRAYS"
3491      description="Number of arrays in the group."
3492      column="narrays"
3493      type="int"
3494      averagemethod="arithmetic_mean"
3495    />
3496    <property
3497      name="ARRAY_STDEV"
3498      title="ARRAY_STDEV"
3499      description="Standard deviation associated with array-to-array variability within the group (undefined when the group contains a single array)."
3500      column="arrayStdDev"
3501      type="float"
3502      averagemethod="arithmetic_mean"
3503    />
3504    <property
3505      name="BEAD_STDEV"
3506      title="BEAD_STDEV"
3507      description="Average standard deviation associated with bead-to-bead variability for the arrays in the group."
3508      column="beadStdDev"
3509      type="float"
3510      averagemethod="arithmetic_mean"
3511    />
3512    <property
3513      name="Avg_NBEADS"
3514      title="Avg_NBEADS"
3515      description="Average number of beads per bead type representing probes for the gene."
3516      column="avgNBeads"
3517      type="int"
3518      averagemethod="arithmetic_mean"
3519    />
3520    <property
3521      name="Detection"
3522      title="Detection"
3523      description="p-value computed from the background model characterizing chance that the target sequence signal was distinguishable from the negative controls."
3524      column="detection"
3525      type="float"
3526      averagemethod="none"
3527    />
3528    <intensity-formula
3529      name="avgSignal"
3530      title="Average signal"
3531      description="Average signal as determined by BeadStudio software."
3532      >
3533      <formula 
3534        channel="1"
3535        expression="raw('AVG_Signal')"
3536      />
3537    </intensity-formula>
3538  </raw-data-type>
3539</raw-data-types>
3540
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