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Last change on this file since 3449 was 3449, checked in by Nicklas Nordborg, 16 years ago
Fixes #572
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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 3449 2007-06-05 07:56:55Z nicklas $
6
7	Copyright (C) 2005-2006 Jari Häkkinen, Nicklas Nordborg
8
9	This file is part of BASE - BioArray Software Environment.
10	Available at http://base.thep.lu.se/
11
12	BASE is free software; you can redistribute it and/or modify it
13	under the terms of the GNU General Public License as published by
14	the Free Software Foundation; either version 2 of the License, or
15	(at your option) any later version.
16
17	BASE is distributed in the hope that it will be useful, but
18	WITHOUT ANY WARRANTY; without even the implied warranty of
19	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20	General Public License for more details.
21
22	You should have received a copy of the GNU General Public License
23	along with this program; if not, write to the Free Software
24	Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
25	02111-1307, USA.
26	-->
27	<raw-data-types>
28
29	<raw-data-type
30	id="genepix"
31	channels="2"
32	name="GenePix"
33	table="RawDataGenePix"
34	>
35	<property
36	name="diameter"
37	title="Spot diameter"
38	description="The diameter of the spot in µm"
39	column="diameter"
40	type="float"
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	/>
50	<property
51	name="ch1FgMean"
52	title="Channel 1 foreground mean"
53	description="The mean of the foreground intensity in channel 1"
54	column="ch1_fg_mean"
55	type="float"
56	channel="1"
57	/>
58	<property
59	name="ch1FgSd"
60	title="Channel 1 foreground standard deviation"
61	description="The standard deviation of the foreground intensity in channel 1"
62	column="ch1_fg_sd"
63	type="float"
64	channel="1"
65	/>
66	<property
67	name="ch1BgMedian"
68	title="Channel 1 background median"
69	description="The median of the background intensity in channel 1"
70	column="ch1_bg_median"
71	type="float"
72	channel="1"
73	/>
74	<property
75	name="ch1BgMean"
76	title="Channel 1 background mean"
77	description="The mean of the background intensity in channel 1"
78	column="ch1_bg_mean"
79	type="float"
80	channel="1"
81	/>
82	<property
83	name="ch1BgSd"
84	title="Channel 1 background standard deviation"
85	description="The standard deviation of the background intensity in channel 1"
86	column="ch1_bg_sd"
87	type="float"
88	channel="1"
89	/>
90	<property
91	name="ch1PercSd1"
92	title="% pixels > 1 standard deviation above backgound"
93	description="Percentage of pixels more than 1 standard deviation
94	above the background intensity in channel 1"
95	column="ch1_perc_sd1"
96	type="int"
97	channel="1"
98	/>
99	<property
100	name="ch1PercSd2"
101	title="% pixels > 2 standard deviations above backgound"
102	description="Percentage of pixels more than 2 standard deviations
103	above the background intensity in channel 1"
104	column="ch1_perc_sd2"
105	type="int"
106	channel="1"
107	/>
108	<property
109	name="ch1PercSat"
110	title="Percent saturated pixels"
111	description="Percentage of saturated pixels in channel 1"
112	column="ch1_perc_sat"
113	type="int"
114	channel="1"
115	/>
116
117	<property
118	name="ch2FgMedian"
119	title="Channel 2 foreground median"
120	description="The median of the foreground intensity in channel 2"
121	column="ch2_fg_median"
122	type="float"
123	channel="2"
124	/>
125	<property
126	name="ch2FgMean"
127	title="Channel 2 foreground mean"
128	description="The mean of the foreground intensity in channel 2"
129	column="ch2_fg_mean"
130	type="float"
131	channel="2"
132	/>
133	<property
134	name="ch2FgSd"
135	title="Channel 2 foreground standard deviation"
136	description="The standard deviation of the foreground intensity in channel 2"
137	column="ch2_fg_sd"
138	type="float"
139	channel="2"
140	/>
141	<property
142	name="ch2BgMedian"
143	title="Channel 2 background median"
144	description="The median of the background intensity in channel 2"
145	column="ch2_bg_median"
146	type="float"
147	channel="2"
148	/>
149	<property
150	name="ch2BgMean"
151	title="Channel 2 background mean"
152	description="The mean of the background intensity in channel 2"
153	column="ch2_bg_mean"
154	type="float"
155	channel="2"
156	/>
157	<property
158	name="ch2BgSd"
159	title="Channel 2 background standard deviation"
160	description="The standard deviation of the background intensity in channel 2"
161	column="ch2_bg_sd"
162	type="float"
163	channel="2"
164	/>
165	<property
166	name="ch2PercSd1"
167	title="% pixels > 1 standard deviation above backgound"
168	description="Percentage of pixels more than 1 standard deviation
169	above the background intensity in channel 2"
170	column="ch2_perc_sd1"
171	type="int"
172	channel="2"
173	/>
174	<property
175	name="ch2PercSd2"
176	title="% pixels > 2 standard deviations above backgound"
177	description="Percentage of pixels more than 2 standard deviations
178	above the background intensity in channel 2"
179	column="ch2_perc_sd2"
180	type="int"
181	channel="2"
182	/>
183	<property
184	name="ch2PercSat"
185	title="Percent saturated pixels"
186	description="Percentage of saturated pixels in channel 2"
187	column="ch2_perc_sat"
188	type="int"
189	channel="2"
190	/>
191
192	<property
193	name="ratiosSd"
194	title="Standard deviation of ratios"
195	description="The geometric standard deviation of the pixel intensity ratios."
196	column="ratios_sd"
197	type="float"
198	/>
199	<property
200	name="rgnRatio"
201	title="Regression ratio"
202	description="The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature."
203	column="rgn_ratio"
204	type="float"
205	/>
206	<property
207	name="rgnR2"
208	title="Rgn R2"
209	description="The coefficient of determination for the current regression value."
210	column="rgn_r2"
211	type="float"
212	/>
213
214	<property
215	name="fgPixels"
216	title="Foreground pixels"
217	description="Number of foreground pixels"
218	column="fg_pixels"
219	type="int"
220	/>
221	<property
222	name="bgPixels"
223	title="Background pixels"
224	description="Number of background pixels"
225	column="bg_pixels"
226	type="int"
227	/>
228	<property
229	name="flags"
230	title="Flags"
231	description="Flags"
232	column="flags"
233	type="int"
234	/>
235	<property
236	name="mValue"
237	title="M value"
238	description="M value"
239	column="m_value"
240	type="float"
241	/>
242	<property
243	name="CV"
244	title="CV"
245	description="CV"
246	column="cv"
247	type="float"
248	/>
249	<intensity-formula
250	name="mean"
251	title="Mean FG - Mean BG"
252	description="Subtract mean background from mean foreground"
253	>
254	<formula
255	channel="1"
256	expression="raw('ch1FgMean') - raw('ch1BgMean')"
257	/>
258	<formula
259	channel="2"
260	expression="raw('ch2FgMean') - raw('ch2BgMean')"
261	/>
262	</intensity-formula>
263	<intensity-formula
264	name="median"
265	title="Median FG - Median BG"
266	description="Subtract meadian background from median foreground"
267	>
268	<formula
269	channel="1"
270	expression="raw('ch1FgMedian') - raw('ch1BgMedian')"
271	/>
272	<formula
273	channel="2"
274	expression="raw('ch2FgMedian') - raw('ch2BgMedian')"
275	/>
276	</intensity-formula>
277	<intensity-formula
278	name="medianmean"
279	title="Median FG - Mean BG"
280	description="Subtract mean background from median foreground"
281	>
282	<formula
283	channel="1"
284	expression="raw('ch1FgMedian') - raw('ch1BgMean')"
285	/>
286	<formula
287	channel="2"
288	expression="raw('ch2FgMedian') - raw('ch2BgMean')"
289	/>
290	</intensity-formula>
291	<intensity-formula
292	name="meanmedian"
293	title="Mean FG - Median BG"
294	description="Subtract median background from mean foreground"
295	>
296	<formula
297	channel="1"
298	expression="raw('ch1FgMean') - raw('ch1BgMedian')"
299	/>
300	<formula
301	channel="2"
302	expression="raw('ch2FgMean') - raw('ch2BgMedian')"
303	/>
304	</intensity-formula>
305	<intensity-formula
306	name="meanfg"
307	title="Mean FG"
308	description="Mean foreground"
309	>
310	<formula
311	channel="1"
312	expression="raw('ch1FgMean')"
313	/>
314	<formula
315	channel="2"
316	expression="raw('ch2FgMean')"
317	/>
318	</intensity-formula>
319	<intensity-formula
320	name="medianfg"
321	title="Median FG"
322	description="Median foreground"
323	>
324	<formula
325	channel="1"
326	expression="raw('ch1FgMedian')"
327	/>
328	<formula
329	channel="2"
330	expression="raw('ch2FgMedian')"
331	/>
332	</intensity-formula>
333	<intensity-formula
334	name="medianfgmeanmedianbg"
335	title="Median FG - Mean(Median BG)"
336	description="Subtract mean of median backgrounds from median foreground"
337	>
338	<formula
339	channel="1"
340	expression="raw('ch1FgMedian') - mean('ch1BgMedian')"
341	/>
342	<formula
343	channel="2"
344	expression="raw('ch2FgMedian') - mean('ch2BgMedian')"
345	/>
346	</intensity-formula>
347	<intensity-formula
348	name="meanfgmeanmeanbg"
349	title="Mean FG - Mean(Mean BG)"
350	description="Subtract mean of mean backgrounds from mean foreground"
351	>
352	<formula
353	channel="1"
354	expression="raw('ch1FgMean') - mean('ch1BgMean')"
355	/>
356	<formula
357	channel="2"
358	expression="raw('ch2FgMean') - mean('ch2BgMean')"
359	/>
360	</intensity-formula>
361	<intensity-formula
362	name="medianfgmeanmeanbg"
363	title="Median FG - Mean(Mean BG)"
364	description="Subtract mean of mean backgrounds from median foreground"
365	>
366	<formula
367	channel="1"
368	expression="raw('ch1FgMedian') - mean('ch1BgMean')"
369	/>
370	<formula
371	channel="2"
372	expression="raw('ch2FgMedian') - mean('ch2BgMean')"
373	/>
374	</intensity-formula>
375	<intensity-formula
376	name="meanfgmeanmedianbg"
377	title="Mean FG - Mean(Median BG)"
378	description="Subtract mean of median backgrounds from mean foreground"
379	>
380	<formula
381	channel="1"
382	expression="raw('ch1FgMean') - mean('ch1BgMedian')"
383	/>
384	<formula
385	channel="2"
386	expression="raw('ch2FgMean') - mean('ch2BgMedian')"
387	/>
388	</intensity-formula>
389	</raw-data-type>
390
391	<raw-data-type
392	id="bzscan"
393	channels="1"
394	name="BZScan"
395	table="RawDataBZScan"
396	>
397	<property
398	name="QImageConst"
399	title="Q(image,const)"
400	description="Spot intensity based on user-provided diameter and measured data."
401	column="q_image_const"
402	type="float"
403	/>
404	<property
405	name="QImageVar"
406	title="Q(image,var)"
407	description="Spot intensity based on computed diameter and measured data."
408	column="q_image_var"
409	type="float"
410	/>
411	<property
412	name="QFitConst"
413	title="Q(fit,const)"
414	description="Spot intensity based on user-provided diameter and theoretical fit to the data."
415	column="q_fit_const"
416	type="float"
417	/>
418	<property
419	name="QFitVar"
420	title="Q(fit,var)"
421	description="Spot intensity based on computed diameter and and theoretical fit to the data."
422	column="q_fit_var"
423	type="float"
424	/>
425	<property
426	name="FitCorrection"
427	title="Fit correction"
428	description="Background level by unit surface."
429	column="fit_correction"
430	type="float"
431	/>
432	<property
433	name="QM"
434	title="Quality metric"
435	description="Quality metric: distance between measured data and theoretical fit."
436	column="quality_metric"
437	type="float"
438	/>
439	<property
440	name="SpotQuality"
441	title="Spot quality"
442	description="Present/Absent (automatic guess)."
443	column="spot_quality"
444	type="boolean"
445	/>
446	<property
447	name="OvershiningCorrection"
448	title="Overshining correction"
449	description="Correction for overshining by unit radius."
450	column="overshining"
451	type="float"
452	/>
453	<intensity-formula
454	name="QImageConst"
455	title="Q(image,const)"
456	description="Spot intensity based on user-provided diameter and measured data"
457	>
458	<formula
459	channel="1"
460	expression="raw('QImageConst')"
461	/>
462	</intensity-formula>
463	<intensity-formula
464	name="QImageVar"
465	title="Q(image,var)"
466	description="Spot intensity based on computed diameter and measured data"
467	>
468	<formula
469	channel="1"
470	expression="raw('QImageVar')"
471	/>
472	</intensity-formula>
473	<intensity-formula
474	name="QFitConst"
475	title="Q(fit,const)"
476	description="Spot intensity based on user-provided diameter and theoretical fit to the data"
477	>
478	<formula
479	channel="1"
480	expression="raw('QFitConst')"
481	/>
482	</intensity-formula>
483	<intensity-formula
484	name="QFitVar"
485	title="Q(fit,var)"
486	description="Spot intensity based on computed diameter and and theoretical fit to the data"
487	>
488	<formula
489	channel="1"
490	expression="raw('QFitVar')"
491	/>
492	</intensity-formula>
493	</raw-data-type>
494
495	<raw-data-type
496	id="aida"
497	channels="2"
498	name="AIDA"
499	table="RawDataAida"
500	>
501	<property
502	name="area"
503	title="Area"
504	description="Spot area in pixels."
505	column="area"
506	type="float"
507	/>
508	<property
509	name="ch1Integral"
510	title="Channel 1 integral"
511	description="Integrated raw intensity of spot channel 1."
512	column="ch1_integral"
513	type="float"
514	channel="1"
515	/>
516	<property
517	name="ch1Mean"
518	title="Channel 1 mean"
519	description="Mean (Integral/Area) channel 1."
520	column="ch1_mean"
521	type="float"
522	channel="1"
523	/>
524	<property
525	name="ch1Median"
526	title="Channel 1 median"
527	description="Median of the raw pixel intensity of spot channel 1."
528	column="ch1_median"
529	type="float"
530	channel="1"
531	/>
532	<property
533	name="ch1Bkg"
534	title="Channel 1 background"
535	description="Standard deviation of background channel 1."
536	column="ch1_bkg"
537	type="float"
538	channel="1"
539	/>
540	<property
541	name="ch1Sat"
542	title="Channel 1 saturated"
543	description="Measure of saturation pixels channel 1."
544	column="ch1_sat"
545	type="float"
546	channel="1"
547	/>
548	<property
549	name="ch1Hom"
550	title="Channel 1 homogenity"
551	description="Percentage of dot deviation from homogenous intensity distribution channel 1."
552	column="ch1_hom"
553	type="float"
554	channel="1"
555	/>
556	<property
557	name="ch1Quality"
558	title="Channel 1 quality"
559	description="Quality flag channel 1."
560	column="ch1_quality"
561	type="boolean"
562	channel="1"
563	/>
564	<property
565	name="ch2Integral"
566	title="Channel 2 integral"
567	description="Integrated raw intensity of spot channel 2."
568	column="ch2_integral"
569	type="float"
570	channel="2"
571	/>
572	<property
573	name="ch2Mean"
574	title="Channel 2 mean"
575	description="Mean (Integral/Area) channel 2."
576	column="ch2_mean"
577	type="float"
578	channel="2"
579	/>
580	<property
581	name="ch2Median"
582	title="Channel 2 median"
583	description="Median of the raw pixel intensity of spot channel 2."
584	column="ch2_median"
585	type="float"
586	channel="2"
587	/>
588	<property
589	name="ch2Bkg"
590	title="Channel 2 background"
591	description="Standard deviation of background channel 2."
592	column="ch2_bkg"
593	type="float"
594	channel="2"
595	/>
596	<property
597	name="ch2Sat"
598	title="Channel 2 saturated"
599	description="Measure of saturation pixels channel 2."
600	column="ch2_sat"
601	type="float"
602	channel="2"
603	/>
604	<property
605	name="ch2Hom"
606	title="Channel 2 homogenity"
607	description="Percentage of dot deviation from homogenous intensity distribution channel 2."
608	column="ch2_hom"
609	type="float"
610	channel="2"
611	/>
612	<property
613	name="ch2Quality"
614	title="Channel 2 quality"
615	description="Quality flag channel 2."
616	column="ch2_quality"
617	type="boolean"
618	channel="2"
619	/>
620	<intensity-formula
621	name="mean"
622	title="Mean"
623	description="Mean of the raw pixel intensity (Integral/Area)"
624	>
625	<formula
626	channel="1"
627	expression="raw('ch1Mean')"
628	/>
629	<formula
630	channel="2"
631	expression="raw('ch2Mean')"
632	/>
633	</intensity-formula>
634	<intensity-formula
635	name="median"
636	title="Median"
637	description="Median of the raw pixel intensity"
638	>
639	<formula
640	channel="1"
641	expression="raw('ch1Median')"
642	/>
643	<formula
644	channel="2"
645	expression="raw('ch2Median')"
646	/>
647	</intensity-formula>
648	</raw-data-type>
649
650	<raw-data-type
651	id="affymetrix"
652	channels="1"
653	name="Affymetrix"
654	storage="file"
655	>
656	</raw-data-type>
657
658	<raw-data-type
659	id="agilent"
660	channels="2"
661	name="Agilent"
662	table="RawDataAgilent"
663	>
664	<property
665	name="LogRatio"
666	title="Log ratio"
667	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 <= 0.0 amp; DyeNormGreenSig > 0.0; 2 if DyeNormRedSig > 0.0 & DyeNormGreenSig <= 0.0; and 0 if DyeNormRedSig <= 0.0 amp; DyeNormGreenSig <= 0.0."
668	column="log_ratio"
669	type="float"
670	/>
671	<property
672	name="PValueLogRatio"
673	title="P value log ratio"
674	description="Significance level of the Log Ratio computed for a feature."
675	column="pvalue_log_ratio"
676	type="float"
677	/>
678	<property
679	name="gSurrogateUsed"
680	title="G surrogate used"
681	description="The green surrogate value used."
682	column="g_surrogate_used"
683	channel="1"
684	type="float"
685	/>
686	<property
687	name="rSurrogateUsed"
688	title="R surrogate used"
689	description="The red surrogate value used."
690	column="r_surrogate_used"
691	channel="2"
692	type="float"
693	/>
694	<property
695	name="gIsFound"
696	title="G is found"
697	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."
698	column="g_is_found"
699	channel="1"
700	type="boolean"
701	/>
702	<property
703	name="rIsFound"
704	title="R is found"
705	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."
706	column="r_is_found"
707	channel="2"
708	type="boolean"
709	/>
710	<property
711	name="gProcessedSignal"
712	title="G processed signal"
713	description="The propagated feature signal, per channel, used for computation of log ratio."
714	column="g_processed_signal"
715	channel="1"
716	type="float"
717	/>
718	<property
719	name="rProcessedSignal"
720	title="R processed signal"
721	description="The propagated feature signal, per channel, used for computation of log ratio."
722	column="r_processed_signal"
723	channel="2"
724	type="float"
725	/>
726	<property
727	name="gNumPixOLHi"
728	title="G high outlier pixels"
729	description="Number of outlier pixels per feature with intensity > 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."
730	column="g_high_outlier_pixels"
731	channel="1"
732	type="int"
733	/>
734	<property
735	name="rNumPixOLHi"
736	title="R high outlier pixels"
737	description="Number of outlier pixels per feature with intensity > 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."
738	column="r_high_outlier_pixels"
739	channel="2"
740	type="int"
741	/>
742	<property
743	name="gNumPixOLLo"
744	title="G low outlier pixels"
745	description="Number of outlier pixels per feature with intensity < 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."
746	column="g_low_outlier_pixels"
747	channel="1"
748	type="int"
749	/>
750	<property
751	name="rNumPixOLLo"
752	title="R low outlier pixels"
753	description="Number of outlier pixels per feature with intensity < 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."
754	column="r_low_outlier_pixels"
755	channel="2"
756	type="int"
757	/>
758	<property
759	name="gNumPix"
760	title="G pixels"
761	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."
762	column="g_pixels"
763	channel="1"
764	type="int"
765	/>
766	<property
767	name="rNumPix"
768	title="R pixels"
769	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."
770	column="r_pixels"
771	channel="2"
772	type="int"
773	/>
774	<property
775	name="gMeanSignal"
776	title="G mean signal"
777	description="Raw mean signal of feature in green channel."
778	column="g_mean_signal"
779	channel="1"
780	type="float"
781	/>
782	<property
783	name="rMeanSignal"
784	title="R mean signal"
785	description="Raw mean signal of feature in red channel."
786	column="r_mean_signal"
787	channel="2"
788	type="float"
789	/>
790	<property
791	name="gMedianSignal"
792	title="G median signal"
793	description="Raw median signal of feature in green channel."
794	column="g_median_signal"
795	channel="1"
796	type="float"
797	/>
798	<property
799	name="rMedianSignal"
800	title="R median signal"
801	description="Raw median signal of feature in red channel."
802	column="r_median_signal"
803	channel="2"
804	type="float"
805	/>
806	<property
807	name="gBGNumPix"
808	title="G background pixels"
809	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."
810	column="g_bg_pixels"
811	channel="1"
812	type="int"
813	/>
814	<property
815	name="rBGNumPix"
816	title="R background pixels"
817	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."
818	column="r_bg_pixels"
819	channel="2"
820	type="int"
821	/>
822	<property
823	name="gBGMeanSignal"
824	title="G mean background"
825	description="Mean local background signal (local to corresponding feature) computed per channel."
826	column="g_bg_mean_signal"
827	channel="1"
828	type="float"
829	/>
830	<property
831	name="rBGMeanSignal"
832	title="R mean background"
833	description="Mean local background signal (local to corresponding feature) computed per channel."
834	column="r_bg_mean_signal"
835	channel="2"
836	type="float"
837	/>
838	<property
839	name="gBGMedianSignal"
840	title="G median background"
841	description="Median local background signal (local to corresponding feature) computed per channel."
842	column="g_bg_median_signal"
843	channel="1"
844	type="float"
845	/>
846	<property
847	name="rBGMedianSignal"
848	title="R median background"
849	description="Median local background signal (local to corresponding feature) computed per channel."
850	column="r_bg_median_signal"
851	channel="2"
852	type="float"
853	/>
854	<property
855	name="gNumSatPix"
856	title="G saturated pixels"
857	description="Total number of saturated pixels per feature, computed per channel."
858	column="g_sat_pixels"
859	channel="1"
860	type="int"
861	/>
862	<property
863	name="rNumSatPix"
864	title="R saturated pixels"
865	description="Total number of saturated pixels per feature, computed per channel."
866	column="r_sat_pixels"
867	channel="2"
868	type="int"
869	/>
870	<property
871	name="gIsSaturated"
872	title="G is saturated"
873	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."
874	column="g_is_saturated"
875	channel="1"
876	type="boolean"
877	/>
878	<property
879	name="rIsSaturated"
880	title="R is saturated"
881	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."
882	column="r_is_saturated"
883	channel="2"
884	type="boolean"
885	/>
886	<property
887	name="PixCorrelation"
888	title="Pix correlation"
889	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."
890	column="pix_correlation"
891	type="float"
892	/>
893	<property
894	name="BGPixCorrelation"
895	title="BG pix correlation"
896	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."
897	column="bg_pix_correlation"
898	type="float"
899	/>
900	<property
901	name="gIsFeatNonUnifOL"
902	title="G non-uniform outlier"
903	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."
904	column="g_nonuniform_outlier"
905	channel="1"
906	type="boolean"
907	/>
908	<property
909	name="rIsFeatNonUnifOL"
910	title="R non-uniform outlier"
911	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."
912	column="r_nonuniform_outlier"
913	channel="2"
914	type="boolean"
915	/>
916	<property
917	name="gIsBGNonUnifOL"
918	title="G bg non-uniform outlier"
919	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."
920	column="g_bg_nonuniform_outlier"
921	channel="1"
922	type="boolean"
923	/>
924	<property
925	name="rIsBGNonUnifOL"
926	title="R bg non-uniform outlier"
927	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."
928	column="r_bg_nonuniform_outlier"
929	channel="2"
930	type="boolean"
931	/>
932	<property
933	name="gIsFeatPopnOL"
934	title="G population outlier"
935	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."
936	column="g_population_outlier"
937	channel="1"
938	type="boolean"
939	/>
940	<property
941	name="rIsFeatPopnOL"
942	title="R population outlier"
943	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."
944	column="r_population_outlier"
945	channel="2"
946	type="boolean"
947	/>
948	<property
949	name="gIsBGPopnOL"
950	title="G bg population outlier"
951	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."
952	column="g_bg_population_outlier"
953	channel="1"
954	type="boolean"
955	/>
956	<property
957	name="rIsBGPopnOL"
958	title="R bg population outlier"
959	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."
960	column="r_bg_population_outlier"
961	channel="2"
962	type="boolean"
963	/>
964	<property
965	name="IsManualFlag"
966	title="Manual flag"
967	description="If a feature has been moved manually this flag will be set to 1."
968	column="manual_flag"
969	type="boolean"
970	/>
971	<property
972	name="gBGSubSignal"
973	title="G net signal"
974	description="The net green signal following the subtraction of the background from the raw mean green signal."
975	column="g_net_signal"
976	channel="1"
977	type="float"
978	/>
979	<property
980	name="rBGSubSignal"
981	title="R net signal"
982	description="The net red signal following the subtraction of the background from the raw mean red signal."
983	column="r_net_signal"
984	channel="2"
985	type="float"
986	/>
987	<property
988	name="BGSubSigCorrelation"
989	title="BG correlation"
990	description="Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space."
991	column="bg_correlation"
992	type="float"
993	/>
994	<property
995	name="gIsPosAndSignif"
996	title="G > 0 and significant"
997	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."
998	column="g_significant"
999	channel="1"
1000	type="boolean"
1001	/>
1002	<property
1003	name="rIsPosAndSignif"
1004	title="R > 0 and significant"
1005	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."
1006	column="r_significant"
1007	channel="2"
1008	type="boolean"
1009	/>
1010	<property
1011	name="gPValFeatEqBG"
1012	title="G p-value"
1013	description="P-value from t-test of significance between green Mean signal and green background."
1014	column="g_pvalue"
1015	channel="1"
1016	type="float"
1017	/>
1018	<property
1019	name="rPValFeatEqBG"
1020	title="R p-value"
1021	description="P-value from t-test of significance between red Mean signal and red background."
1022	column="r_pvalue"
1023	channel="2"
1024	type="float"
1025	/>
1026	<property
1027	name="gNumBGUsed"
1028	title="G background pixels"
1029	description="A count of the number of background pixels used in the green channel."
1030	column="g_numbg_used"
1031	channel="1"
1032	type="int"
1033	/>
1034	<property
1035	name="rNumBGUsed"
1036	title="R background pixels"
1037	description="A count of the number of background pixels used in the red channel."
1038	column="r_numbg_used"
1039	channel="2"
1040	type="int"
1041	/>
1042	<property
1043	name="gIsWellAboveBG"
1044	title="G well above bg"
1045	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."
1046	column="g_above_bg"
1047	channel="1"
1048	type="boolean"
1049	/>
1050	<property
1051	name="rIsWellAboveBG"
1052	title="R well above bg"
1053	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."
1054	column="r_above_bg"
1055	channel="2"
1056	type="boolean"
1057	/>
1058	<property
1059	name="gBGUsed"
1060	title="G bg used"
1061	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."
1062	column="g_bg_used"
1063	channel="1"
1064	type="float"
1065	/>
1066	<property
1067	name="rBGUsed"
1068	title="R bg used"
1069	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."
1070	column="r_bg_used"
1071	channel="2"
1072	type="float"
1073	/>
1074	<property
1075	name="IsNormalization"
1076	title="Normalization"
1077	description="A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used."
1078	column="is_normalization"
1079	type="boolean"
1080	/>
1081	<property
1082	name="gDyeNormSignal"
1083	title="G normalized signal"
1084	description="The dye normalized signal in the green channel."
1085	column="g_normalized"
1086	channel="1"
1087	type="float"
1088	/>
1089	<property
1090	name="rDyeNormSignal"
1091	title="R normalized signal"
1092	description="The dye normalized signal in the green channel."
1093	column="r_normalized"
1094	channel="2"
1095	type="float"
1096	/>
1097	<property
1098	name="DyeNormCorrelation"
1099	title="Normalized correlation"
1100	description="Dye normalized red and green pixel correlation."
1101	column="norm_correlation"
1102	type="float"
1103	/>
1104	<property
1105	name="ErrorModel"
1106	title="Error model"
1107	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."
1108	column="error_model"
1109	type="int"
1110	/>
1111	<property
1112	name="xDev"
1113	title="X dev"
1114	description="Used to compute the Log Ratio PValue."
1115	column="x_dev"
1116	type="float"
1117	/>
1118	<property
1119	name="gSpatialDetrendIsInFilteredSet"
1120	title="G spatial trend"
1121	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."
1122	column="g_spatial_trend"
1123	channel="1"
1124	type="boolean"
1125	/>
1126	<property
1127	name="rSpatialDetrendIsInFilteredSet"
1128	title="R spatial trend"
1129	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."
1130	column="r_spatial_trend"
1131	channel="2"
1132	type="boolean"
1133	/>
1134	<property
1135	name="gSpatialDetrendSurfaceValue"
1136	title="G surface value"
1137	description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1138	column="g_surface_value"
1139	channel="1"
1140	type="float"
1141	/>
1142	<property
1143	name="rSpatialDetrendSurfaceValue"
1144	title="R surface value"
1145	description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
1146	column="r_surface_value"
1147	channel="2"
1148	type="float"
1149	/>
1150	<intensity-formula
1151	name="mean"
1152	title="Mean FG - Mean BG"
1153	description="Subtract mean background from mean foreground"
1154	>
1155	<formula
1156	channel="1"
1157	expression="raw('gMeanSignal') - raw('gBGMeanSignal')"
1158	/>
1159	<formula
1160	channel="2"
1161	expression="raw('rMeanSignal') - raw('rBGMeanSignal')"
1162	/>
1163	</intensity-formula>
1164	<intensity-formula
1165	name="median"
1166	title="Median FG - Median BG"
1167	description="Subtract meadian background from median foreground"
1168	>
1169	<formula
1170	channel="1"
1171	expression="raw('gMedianSignal') - raw('gBGMedianSignal')"
1172	/>
1173	<formula
1174	channel="2"
1175	expression="raw('rMedianSignal') - raw('rBGMedianSignal')"
1176	/>
1177	</intensity-formula>
1178	<intensity-formula
1179	name="medianmean"
1180	title="Median FG - Mean BG"
1181	description="Subtract mean background from median foreground"
1182	>
1183	<formula
1184	channel="1"
1185	expression="raw('gMedianSignal') - raw('gBGMeanSignal')"
1186	/>
1187	<formula
1188	channel="2"
1189	expression="raw('rMedianSignal') - raw('rBGMeanSignal')"
1190	/>
1191	</intensity-formula>
1192	<intensity-formula
1193	name="meanmedian"
1194	title="Mean FG - Median BG"
1195	description="Subtract median background from mean foreground"
1196	>
1197	<formula
1198	channel="1"
1199	expression="raw('gMeanSignal') - raw('gBGMedianSignal')"
1200	/>
1201	<formula
1202	channel="2"
1203	expression="raw('rMeanSignal') - raw('rBGMedianSignal')"
1204	/>
1205	</intensity-formula>
1206	<intensity-formula
1207	name="meanfg"
1208	title="Mean FG"
1209	description="Mean foreground"
1210	>
1211	<formula
1212	channel="1"
1213	expression="raw('gMeanSignal')"
1214	/>
1215	<formula
1216	channel="2"
1217	expression="raw('rMeanSignal')"
1218	/>
1219	</intensity-formula>
1220	<intensity-formula
1221	name="medianfg"
1222	title="Median FG"
1223	description="Median foreground"
1224	>
1225	<formula
1226	channel="1"
1227	expression="raw('gMedianSignal')"
1228	/>
1229	<formula
1230	channel="2"
1231	expression="raw('rMedianSignal')"
1232	/>
1233	</intensity-formula>
1234	<intensity-formula
1235	name="medianfgmeanmedianbg"
1236	title="Median FG - Mean(Median BG)"
1237	description="Subtract mean of median backgrounds from median foreground"
1238	>
1239	<formula
1240	channel="1"
1241	expression="raw('gMedianSignal') - mean('gBGMedianSignal')"
1242	/>
1243	<formula
1244	channel="2"
1245	expression="raw('rMedianSignal') - mean('rBGMedianSignal')"
1246	/>
1247	</intensity-formula>
1248	<intensity-formula
1249	name="meanfgmeanmeanbg"
1250	title="Mean FG - Mean(Mean BG)"
1251	description="Subtract mean of mean backgrounds from mean foreground"
1252	>
1253	<formula
1254	channel="1"
1255	expression="raw('gMeanSignal') - mean('gBGMeanSignal')"
1256	/>
1257	<formula
1258	channel="2"
1259	expression="raw('rMeanSignal') - mean('rBGMeanSignal')"
1260	/>
1261	</intensity-formula>
1262	<intensity-formula
1263	name="medianfgmeanmeanbg"
1264	title="Median FG - Mean(Mean BG)"
1265	description="Subtract mean of mean backgrounds from median foreground"
1266	>
1267	<formula
1268	channel="1"
1269	expression="raw('gMedianSignal') - mean('gBGMeanSignal')"
1270	/>
1271	<formula
1272	channel="2"
1273	expression="raw('rMedianSignal') - mean('rBGMeanSignal')"
1274	/>
1275	</intensity-formula>
1276	<intensity-formula
1277	name="meanfgmeanmedianbg"
1278	title="Mean FG - Mean(Median BG)"
1279	description="Subtract mean of median backgrounds from mean foreground"
1280	>
1281	<formula
1282	channel="1"
1283	expression="raw('gMeanSignal') - mean('gBGMedianSignal')"
1284	/>
1285	<formula
1286	channel="2"
1287	expression="raw('rMeanSignal') - mean('rBGMedianSignal')"
1288	/>
1289	</intensity-formula>
1290	</raw-data-type>
1291
1292	<raw-data-type
1293	id="chipskipper"
1294	channels="2"
1295	name="ChipSkipper"
1296	table="RawDataChipSkipper"
1297	>
1298	<property
1299	name="Line_Counter"
1300	title="Line counter"
1301	description="Line counter."
1302	column="line_counter"
1303	type="int"
1304	/>
1305	<property
1306	name="Flags"
1307	title="Flags"
1308	description="Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad."
1309	column="flags"
1310	type="string"
1311	/>
1312	<property
1313	name="GS_Flags"
1314	title="GS flags"
1315	description="P = pass or M = marginal flag."
1316	column="gs_flags"
1317	type="string"
1318	/>
1319	<property
1320	name="Cy3_Volume"
1321	title="Cy3 volume"
1322	description="Total integrated signal intensity in color channel Cy3."
1323	column="cy3_volume"
1324	channel="1"
1325	type="int"
1326	/>
1327	<property
1328	name="Cy3_AvVolpixel"
1329	title="Cy3 average intensity"
1330	description="Average intensity per pixel in color channel Cy3."
1331	column="cy3_avg"
1332	channel="1"
1333	type="float"
1334	/>
1335	<property
1336	name="Cy3_BGArith"
1337	title="Cy3 background (arithmetic)"
1338	description="Arithmetic average for local background in color channel Cy3."
1339	column="cy3_bg_arith"
1340	channel="1"
1341	type="float"
1342	/>
1343	<property
1344	name="Cy3_BGGeom"
1345	title="Cy3 background (geometric)"
1346	description="Geometric average for local background in color channel Cy3."
1347	column="cy3_bg_geom"
1348	channel="1"
1349	type="float"
1350	/>
1351	<property
1352	name="Cy3_BGMedian"
1353	title="Cy3 background (median)"
1354	description="Median average for local background in color channel Cy3."
1355	column="cy3_bg_median"
1356	channel="1"
1357	type="float"
1358	/>
1359	<property
1360	name="Cy3_BG_Tot"
1361	title="Cy3 background (total)"
1362	description="Total integrated background in color channel Cy3."
1363	column="cy3_bg_total"
1364	channel="1"
1365	type="float"
1366	/>
1367	<property
1368	name="Cy3_VolBG"
1369	title="Cy3 reduced intensity"
1370	description="Background reduced intensity of colour channel Cy3."
1371	column="cy3_reduced"
1372	channel="1"
1373	type="float"
1374	/>
1375	<property
1376	name="Cy3_Spotarea"
1377	title="Cy3 spot area"
1378	description="Area of spot in colour channel Cy3 in pixels."
1379	column="cy3_area"
1380	channel="1"
1381	type="float"
1382	/>
1383	<property
1384	name="Cy3_Satpixel"
1385	title="Cy3 saturated pixels"
1386	description="Number of saturated pixel in color channel Cy3."
1387	column="cy3_saturated"
1388	channel="1"
1389	type="float"
1390	/>
1391	<property
1392	name="Cy5_Volume"
1393	title="Cy5 volume"
1394	description="Total integrated signal intensity in color channel Cy5."
1395	column="cy5_volume"
1396	channel="2"
1397	type="int"
1398	/>
1399	<property
1400	name="Cy5_AvVolpixel"
1401	title="Cy5 average intensity"
1402	description="Average intensity per pixel in color channel Cy5."
1403	column="cy5_avg"
1404	channel="2"
1405	type="float"
1406	/>
1407	<property
1408	name="Cy5_BGArith"
1409	title="Cy5 background (arithmetic)"
1410	description="Arithmetic average for local background in color channel Cy5."
1411	column="cy5_bg_arith"
1412	channel="2"
1413	type="float"
1414	/>
1415	<property
1416	name="Cy5_BGGeom"
1417	title="Cy5 background (geometric)"
1418	description="Geometric average for local background in color channel Cy5."
1419	column="cy5_bg_geom"
1420	channel="2"
1421	type="float"
1422	/>
1423	<property
1424	name="Cy5_BGMedian"
1425	title="Cy5 background (median)"
1426	description="Median average for local background in color channel Cy5."
1427	column="cy5_bg_median"
1428	channel="2"
1429	type="float"
1430	/>
1431	<property
1432	name="Cy5_BG_Tot"
1433	title="Cy5 background (total)"
1434	description="Total integrated background in color channel Cy5."
1435	column="cy5_bg_total"
1436	channel="2"
1437	type="float"
1438	/>
1439	<property
1440	name="Cy5_VolBG"
1441	title="Cy5 reduced intensity"
1442	description="Background reduced intensity of colour channel Cy5."
1443	column="cy5_reduced"
1444	channel="2"
1445	type="float"
1446	/>
1447	<property
1448	name="Cy5_Spotarea"
1449	title="Cy5 spot area"
1450	description="Area of spot in colour channel Cy5 in pixels."
1451	column="cy5_area"
1452	channel="2"
1453	type="float"
1454	/>
1455	<property
1456	name="Cy5_Satpixel"
1457	title="Cy5 saturated pixels"
1458	description="Number of saturated pixel in color channel Cy5."
1459	column="cy5_saturated"
1460	channel="2"
1461	type="float"
1462	/>
1463	<property
1464	name="Rep_vol_BG2"
1465	title="Background reduced volume"
1466	description="Average of background reduced volume for onchip replicas (when calculated)."
1467	column="rep_vol"
1468	type="float"
1469	/>
1470	<property
1471	name="RatioCy5Cy3"
1472	title="Direct ratio"
1473	description="Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )."
1474	column="ratio"
1475	type="float"
1476	/>
1477	<property
1478	name="Directional_RatioCy5Cy3"
1479	title="Directional ratio"
1480	description="Directional ratio: if Ratio > 1 then Directional = Ratio, if Ratio > 1 then Directional = -1/Ratio."
1481	column="directional_ratio"
1482	type="float"
1483	/>
1484	<property
1485	name="Log2_RatioCy5Cy3"
1486	title="Log2 ratio"
1487	description="Log2 ratio: log2 (Ratio-Cy5/Cy3)"
1488	column="log2_ratio"
1489	type="float"
1490	/>
1491	<property
1492	name="Comp_ChannelCy3"
1493	title="Cy53 normalised intensity"
1494	description="Normalised intensity of Cy3_Vol-BG."
1495	column="cy3_normalised"
1496	channel="1"
1497	type="float"
1498	/>
1499	<property
1500	name="Comp_ChannelCy5"
1501	title="Cy5 normalised intensity"
1502	description="Normalised intensity of Cy5_Vol-BG."
1503	column="cy5_normalised"
1504	channel="2"
1505	type="float"
1506	/>
1507	<property
1508	name="Comp_RatioCy5Cy3"
1509	title="Compensated ratio"
1510	description="Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 )."
1511	column="compensated_ratio"
1512	type="float"
1513	/>
1514	<property
1515	name="Comp_Directional_RatioCy5Cy3"
1516	title="Compensated directional ratio"
1517	description="Compensated directional ratio: if Comp_Ratio > 1 then Directional = Ratio, if Ratio < 1 then Directional = -1/Ratio."
1518	column="comp_dir_ratio"
1519	type="float"
1520	/>
1521	<property
1522	name="Comp_Log2_Ratio"
1523	title="Compensated log2 ratio"
1524	description="Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3)."
1525	column="comp_log2_ratio"
1526	type="float"
1527	/>
1528	<property
1529	name="Comment"
1530	title="Comment"
1531	description="Additional description of spot."
1532	column="comment"
1533	type="string"
1534	/>
1535	<property
1536	name="SNRtot"
1537	title="Squared average SNR"
1538	description="Squared average of Cy5_SNR and Cy3_SNR."
1539	column="snr_tot"
1540	type="float"
1541	/>
1542	<property
1543	name="SNRtot_Score"
1544	title="Squared average score SNR"
1545	description="Squared average of Cy5_%SNR and Cy3_%SNR."
1546	column="snr_tot_score"
1547	type="float"
1548	/>
1549	<property
1550	name="SNRGS"
1551	title="Saturated pixel"
1552	description="Number of saturated pixel in both colors (logical or)."
1553	column="sat_pixels"
1554	type="float"
1555	/>
1556	<property
1557	name="Replicas"
1558	title="Replicas"
1559	description="Replicas"
1560	column="replicas"
1561	type="float"
1562	/>
1563	<property
1564	name="Regulation"
1565	title="Regulation"
1566	description="If Flag = SNR1 then Regulation=>Down; if Flag = SNR2 then Regulation=>up; if Flag = SNR1 AND SNR2 then Regulation=>>weak; else Regulation = Ratio-Cy5/Cy3."
1567	column="regulation"
1568	type="string"
1569	/>
1570	<property
1571	name="GroupName"
1572	title="Group name"
1573	description="Group name for this spot."
1574	column="group_name"
1575	type="string"
1576	/>
1577	<property
1578	name="MedianRatios"
1579	title="Median of ratios"
1580	description="Median of ratios (Cy5/Cy3) from all pixel in this spot."
1581	column="median_ratios"
1582	type="float"
1583	/>
1584	<property
1585	name="MedianRatiosSDev"
1586	title="Median of ratios (sdev%)"
1587	description="Standard deviation of Median of ratios in percent."
1588	column="median_ratios_sdev"
1589	type="float"
1590	/>
1591	<property
1592	name="RatioMedians"
1593	title="Ratio of medians"
1594	description="Ratio of Medians (Cy5/Cy3) from all pixel in this spot."
1595	column="ratio_medians"
1596	type="float"
1597	/>
1598	<property
1599	name="RatioMediansSDev"
1600	title="Ratio of medians (sdev%)"
1601	description="Standard deviation of Ratio of medians in percent."
1602	column="ratio_medians_sdev"
1603	type="float"
1604	/>
1605	<intensity-formula
1606	name="Volume"
1607	title="Volume"
1608	description="Total integrated signal intensity"
1609	>
1610	<formula
1611	channel="1"
1612	expression="raw('Cy3_Volume')"
1613	/>
1614	<formula
1615	channel="2"
1616	expression="raw('Cy5_Volume')"
1617	/>
1618	</intensity-formula>
1619	<intensity-formula
1620	name="VolBG"
1621	title="Reduced intensity"
1622	description="Background reduced intensity"
1623	>
1624	<formula
1625	channel="1"
1626	expression="raw('Cy3_VolBG')"
1627	/>
1628	<formula
1629	channel="2"
1630	expression="raw('Cy5_VolBG')"
1631	/>
1632	</intensity-formula>
1633	</raw-data-type>
1634
1635	<raw-data-type
1636	id="genetac"
1637	channels="2"
1638	name="GeneTAC"
1639	table="RawDataGeneTac"
1640	>
1641	<property
1642	name="medCy3"
1643	title="Signal median Cy3"
1644	description="Median of Cy3 signal intensity."
1645	column="med_cy3"
1646	channel="1"
1647	type="float"
1648	/>
1649	<property
1650	name="medCy5"
1651	title="Signal median Cy5"
1652	description="Median of Cy5 signal intensity."
1653	column="med_cy5"
1654	channel="2"
1655	type="float"
1656	/>
1657	<property
1658	name="medRatio"
1659	title="Signal median ratio"
1660	description="Ratio of median signal."
1661	column="med_ratio"
1662	type="float"
1663	/>
1664	<property
1665	name="bgCy3"
1666	title="Background median Cy3"
1667	description="Median of background intensity for Cy3."
1668	column="bg_cy3"
1669	channel="1"
1670	type="float"
1671	/>
1672	<property
1673	name="bgCy5"
1674	title="Background median Cy5"
1675	description="Median of background intensity for Cy5."
1676	column="bg_cy5"
1677	channel="2"
1678	type="float"
1679	/>
1680	<property
1681	name="bgRatio"
1682	title="Signal med ratio"
1683	description="Ratio of median background."
1684	column="bg_ratio"
1685	type="float"
1686	/>
1687	<intensity-formula
1688	name="medianfg"
1689	title="Median FG"
1690	description="Median foreground"
1691	>
1692	<formula
1693	channel="1"
1694	expression="raw('medCy3')"
1695	/>
1696	<formula
1697	channel="2"
1698	expression="raw('medCy5')"
1699	/>
1700	</intensity-formula>
1701	<intensity-formula
1702	name="median"
1703	title="Median FG - Median BG"
1704	description="Subtract median background from median foreground"
1705	>
1706	<formula
1707	channel="1"
1708	expression="raw('medCy3') - raw('bgCy3')"
1709	/>
1710	<formula
1711	channel="2"
1712	expression="raw('medCy5') - raw('bgCy5')"
1713	/>
1714	</intensity-formula>
1715	</raw-data-type>
1716
1717	<raw-data-type
1718	id="imagene"
1719	channels="2"
1720	name="ImaGene"
1721	table="RawDataImaGene"
1722	>
1723	<property
1724	name="Field"
1725	title="Field"
1726	description="Name of a field where the spot is located."
1727	column="field"
1728	type="string"
1729	/>
1730	<property
1731	name="Flag_Cy3"
1732	title="Flag cy3"
1733	description="Numeric code for the spot (0 - no flag, flag codes 1,...,7)."
1734	column="cy3_flag"
1735	channel="1"
1736	type="int"
1737	/>
1738	<property
1739	name="SignalMean_Cy3"
1740	title="Mean signal cy3"
1741	description="Pixel intensity averaged over the local signal region."
1742	column="cy3_mean_signal"
1743	channel="1"
1744	type="float"
1745	/>
1746	<property
1747	name="BackgroundMean_Cy3"
1748	title="Mean background cy3"
1749	description="Pixel intensity averaged over the local background region."
1750	column="cy3_mean_bg"
1751	channel="1"
1752	type="float"
1753	/>
1754	<property
1755	name="SignalMedian_Cy3"
1756	title="Median signal cy3"
1757	description="Median pixel intensity computed over the local signal region."
1758	column="cy3_median_signal"
1759	channel="1"
1760	type="float"
1761	/>
1762	<property
1763	name="BackgroundMedian_Cy3"
1764	title="Median background cy3"
1765	description="Median pixel intensity averaged over the local background region."
1766	column="cy3_median_bg"
1767	channel="1"
1768	type="float"
1769	/>
1770	<property
1771	name="SignalMode_Cy3"
1772	title="Mode signal cy3"
1773	description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
1774	column="cy3_mode_signal"
1775	channel="1"
1776	type="float"
1777	/>
1778	<property
1779	name="BackgroundMode_Cy3"
1780	title="Mode background cy3"
1781	description="Mode pixel intensity computed over the local background region."
1782	column="cy3_mode_bg"
1783	channel="1"
1784	type="float"
1785	/>
1786	<property
1787	name="SignalArea_Cy3"
1788	title="Signal area cy3"
1789	description="Number of pixels in the local signal region."
1790	column="cy3_area_signal"
1791	channel="1"
1792	type="int"
1793	/>
1794	<property
1795	name="BackgroundArea_Cy3"
1796	title="Background area cy3"
1797	description="Number of pixels in the local background region."
1798	column="cy3_area_bg"
1799	channel="1"
1800	type="int"
1801	/>
1802	<property
1803	name="SignalTotal_Cy3"
1804	title="Total signal cy3"
1805	description="Total pixel intensity summed over the local signal region."
1806	column="cy3_total_signal"
1807	channel="1"
1808	type="int"
1809	/>
1810	<property
1811	name="BackgroundTotal_Cy3"
1812	title="Total background cy3"
1813	description="Total pixel intensity summed over the local background region."
1814	column="cy3_total_bg"
1815	channel="1"
1816	type="int"
1817	/>
1818	<property
1819	name="ShapeRegularity_Cy3"
1820	title="Shape regularity cy3"
1821	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."
1822	column="cy3_shape"
1823	channel="1"
1824	type="float"
1825	/>
1826	<property
1827	name="IgnoredArea_Cy3"
1828	title="Ignored area cy3"
1829	description="Area of ignored regions directly neighboring (touching) the signal area is computed."
1830	column="cy3_area_ignored"
1831	channel="1"
1832	type="int"
1833	/>
1834	<property
1835	name="SpotArea_Cy3"
1836	title="Spot area cy3"
1837	description="Signal Area plus Ignored Area."
1838	column="cy3_area_spot"
1839	channel="1"
1840	type="int"
1841	/>
1842	<property
1843	name="IgnoredMedian_Cy3"
1844	title="Median ignored cy3"
1845	description="Median pixel intensity computed over the local ignored region."
1846	column="cy3_median_ignored"
1847	channel="1"
1848	type="float"
1849	/>
1850	<property
1851	name="AreaToPerimeter_Cy3"
1852	title="Area to perimeter cy3"
1853	description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4π. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
1854	column="cy3_area_perimeter"
1855	channel="1"
1856	type="float"
1857	/>
1858	<property
1859	name="OpenPerimeter_Cy3"
1860	title="Open perimeter cy3"
1861	description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
1862	column="cy3_open_perimeter"
1863	channel="1"
1864	type="float"
1865	/>
1866	<property
1867	name="XCoord_Cy3"
1868	title="X coordinate cy3"
1869	description="X coordinate (in pixels) of grid circle corresponding to the spot."
1870	column="cy3_x"
1871	channel="1"
1872	type="float"
1873	/>
1874	<property
1875	name="YCoord_Cy3"
1876	title="Y coordinate cy3"
1877	description="Y coordinate (in pixels) of grid circle corresponding to the spot."
1878	column="cy3_y"
1879	channel="1"
1880	type="float"
1881	/>
1882	<property
1883	name="Diameter_Cy3"
1884	title="Diameter cy3"
1885	description="Diameter (in pixels) of grid circle corresponding to the spot."
1886	column="cy3_diameter"
1887	channel="1"
1888	type="int"
1889	/>
1890	<property
1891	name="PositionOffset_Cy3"
1892	title="Position offset cy3"
1893	description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
1894	column="cy3_offset"
1895	channel="1"
1896	type="float"
1897	/>
1898	<property
1899	name="OffsetX_Cy3"
1900	title="X offset cy3"
1901	description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
1902	column="cy3_offset_x"
1903	channel="1"
1904	type="float"
1905	/>
1906	<property
1907	name="OffsetY_Cy3"
1908	title="Y offset cy3"
1909	description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
1910	column="cy3_offset_y"
1911	channel="1"
1912	type="float"
1913	/>
1914	<property
1915	name="ExpectedX_Cy3"
1916	title="X expected cy3"
1917	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."
1918	column="cy3_x_expected"
1919	channel="1"
1920	type="float"
1921	/>
1922	<property
1923	name="ExpectedY_Cy3"
1924	title="Y expected cy3"
1925	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."
1926	column="cy3_y_expected"
1927	channel="1"
1928	type="float"
1929	/>
1930	<property
1931	name="CMX_Cy3"
1932	title="CM X coordinate cy3"
1933	description="X coordinate of the center of the mass of spot's signal region."
1934	column="cy3_x_cm"
1935	channel="1"
1936	type="float"
1937	/>
1938	<property
1939	name="CMY_Cy3"
1940	title="CM Y coordinate cy3"
1941	description="Y coordinate of the center of the mass of spot's signal region."
1942	column="cy3_y_cm"
1943	channel="1"
1944	type="float"
1945	/>
1946	<property
1947	name="CMOffset_Cy3"
1948	title="CM offset cy3"
1949	description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
1950	column="cy3_offset_cm"
1951	channel="1"
1952	type="float"
1953	/>
1954	<property
1955	name="CMOffsetX_Cy3"
1956	title="CM X offset cy3"
1957	description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
1958	column="cy3_offset_x_cm"
1959	channel="1"
1960	type="float"
1961	/>
1962	<property
1963	name="CMOffsetY_Cy3"
1964	title="CM Y offset cy3"
1965	description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
1966	column="cy3_offset_y_cm"
1967	channel="1"
1968	type="float"
1969	/>
1970	<property
1971	name="MinDiam_Cy3"
1972	title="Min diameter cy3"
1973	description="Diameter of the circle inscribed into the spot's signal region."
1974	column="cy3_diameter_min"
1975	channel="1"
1976	type="float"
1977	/>
1978	<property
1979	name="MaxDiam_Cy3"
1980	title="Max diameter cy3"
1981	description="Diameter of the circle, the spot's signal region can be inscribed in."
1982	column="cy3_diameter_max"
1983	channel="1"
1984	type="float"
1985	/>
1986	<property
1987	name="Control_Cy3"
1988	title="Control cy3"
1989	description="Name of a control type for current spot (no name means the spot is not a control spot)."
1990	column="cy3_control"
1991	channel="1"
1992	type="string"
1993	/>
1994	<property
1995	name="FailedControl_Cy3"
1996	title="Failed control cy3"
1997	description="0 if the control passed all tests, 1 if at least one of the tests failed."
1998	column="cy3_control_failed"
1999	channel="1"
2000	type="boolean"
2001	/>
2002	<property
2003	name="BackgroundContaminationPresent_Cy3"
2004	title="Bg contamination cy3"
2005	description="0 if the spot passed background contamination test, 1 if it did not."
2006	column="cy3_bg_contamination"
2007	channel="1"
2008	type="boolean"
2009	/>
2010	<property
2011	name="SignalContaminationPresent_Cy3"
2012	title="Signal contamination cy3"
2013	description="0 if the spot passed signal contamination test, 1 if it did not."
2014	column="cy3_signal_contamination"
2015	channel="1"
2016	type="boolean"
2017	/>
2018	<property
2019	name="IgnoredFailed_Cy3"
2020	title="Ignored % failed cy3"
2021	description="0 if the spot passed ignored percentage test, 1 if it did not."
2022	column="cy3_ignored_failed"
2023	channel="1"
2024	type="boolean"
2025	/>
2026	<property
2027	name="OpenPerimeterFailed_Cy3"
2028	title="Open perimeter failed cy3"
2029	description="0 if the spot passed open perimeter test, 1 if it did not."
2030	column="cy3_perimeter_failed"
2031	channel="1"
2032	type="boolean"
2033	/>
2034	<property
2035	name="ShapeRegularityFailed_Cy3"
2036	title="Shape regularity failed cy3"
2037	description="0 if the spot passed shape regularity test, 1 if it did not."
2038	column="cy3_shape_failed"
2039	channel="1"
2040	type="boolean"
2041	/>
2042	<property
2043	name="PerimToAreaFailed_Cy3"
2044	title="Perimeter to area failed cy3"
2045	description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2046	column="cy3_areapm_failed"
2047	channel="1"
2048	type="boolean"
2049	/>
2050	<property
2051	name="OffsetFailed_Cy3"
2052	title="Offset failed cy3"
2053	description="0 if the spot passed offset test, 1 if it did not."
2054	column="cy3_offset_failed"
2055	channel="1"
2056	type="boolean"
2057	/>
2058	<property
2059	name="EmptySpot_Cy3"
2060	title="Empty spot cy3"
2061	description="1 if the spot is empty, 0 if not."
2062	column="cy3_empty_spot"
2063	channel="1"
2064	type="boolean"
2065	/>
2066	<property
2067	name="NegativeSpot_Cy3"
2068	title="Negative spot cy3"
2069	description="1 if the spot was qualified as negative, 0 if it was not."
2070	column="cy3_negative_spot"
2071	channel="1"
2072	type="boolean"
2073	/>
2074	<property
2075	name="SelectedSpot_Cy3"
2076	title="Selected spot cy3"
2077	description="1 if the spot was selected in the software view at time of save, 0 if not."
2078	column="cy3_selected_spot"
2079	channel="1"
2080	type="boolean"
2081	/>
2082	<property
2083	name="SaturatedSpot_Cy3"
2084	title="Saturated spot cy3"
2085	description="1 if the spot was qualified as saturated, 0 if it was not."
2086	column="cy3_saturated_spot"
2087	channel="1"
2088	type="boolean"
2089	/>
2090	<property
2091	name="SignalMean_Cy5"
2092	title="Mean signal cy5"
2093	description="Pixel intensity averaged over the local signal region."
2094	column="cy5_mean_signal"
2095	channel="2"
2096	type="float"
2097	/>
2098	<property
2099	name="BackgroundMean_Cy5"
2100	title="Mean background cy5"
2101	description="Pixel intensity averaged over the local background region."
2102	column="cy5_mean_bg"
2103	channel="2"
2104	type="float"
2105	/>
2106	<property
2107	name="SignalMedian_Cy5"
2108	title="Median signal cy5"
2109	description="Median pixel intensity computed over the local signal region."
2110	column="cy5_median_signal"
2111	channel="2"
2112	type="float"
2113	/>
2114	<property
2115	name="BackgroundMedian_Cy5"
2116	title="Median background cy5"
2117	description="Median pixel intensity averaged over the local background region."
2118	column="cy5_median_bg"
2119	channel="2"
2120	type="float"
2121	/>
2122	<property
2123	name="SignalMode_Cy5"
2124	title="Mode signal cy5"
2125	description="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution)."
2126	column="cy5_mode_signal"
2127	channel="2"
2128	type="float"
2129	/>
2130	<property
2131	name="BackgroundMode_Cy5"
2132	title="Mode background cy5"
2133	description="Mode pixel intensity computed over the local background region."
2134	column="cy5_mode_bg"
2135	channel="2"
2136	type="float"
2137	/>
2138	<property
2139	name="SignalArea_Cy5"
2140	title="Signal area cy5"
2141	description="Number of pixels in the local signal region."
2142	column="cy5_area_signal"
2143	channel="2"
2144	type="int"
2145	/>
2146	<property
2147	name="BackgroundArea_Cy5"
2148	title="Background area cy5"
2149	description="Number of pixels in the local background region."
2150	column="cy5_area_bg"
2151	channel="2"
2152	type="int"
2153	/>
2154	<property
2155	name="SignalTotal_Cy5"
2156	title="Total signal cy5"
2157	description="Total pixel intensity summed over the local signal region."
2158	column="cy5_total_signal"
2159	channel="2"
2160	type="int"
2161	/>
2162	<property
2163	name="BackgroundTotal_Cy5"
2164	title="Total background cy5"
2165	description="Total pixel intensity summed over the local background region."
2166	column="cy5_total_bg"
2167	channel="2"
2168	type="int"
2169	/>
2170	<property
2171	name="ShapeRegularity_Cy5"
2172	title="Shape regularity cy5"
2173	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."
2174	column="cy5_shape"
2175	channel="2"
2176	type="float"
2177	/>
2178	<property
2179	name="IgnoredArea_Cy5"
2180	title="Ignored area cy5"
2181	description="Area of ignored regions directly neighboring (touching) the signal area is computed."
2182	column="cy5_area_ignored"
2183	channel="2"
2184	type="int"
2185	/>
2186	<property
2187	name="SpotArea_Cy5"
2188	title="Spot area cy5"
2189	description="Signal Area plus Ignored Area."
2190	column="cy5_area_spot"
2191	channel="2"
2192	type="int"
2193	/>
2194	<property
2195	name="IgnoredMedian_Cy5"
2196	title="Median ignored cy5"
2197	description="Median pixel intensity computed over the local ignored region."
2198	column="cy5_median_ignored"
2199	channel="2"
2200	type="float"
2201	/>
2202	<property
2203	name="AreaToPerimeter_Cy5"
2204	title="Area to perimeter cy5"
2205	description="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4π. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle)."
2206	column="cy5_area_perimeter"
2207	channel="2"
2208	type="float"
2209	/>
2210	<property
2211	name="OpenPerimeter_Cy5"
2212	title="Open perimeter cy5"
2213	description="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot."
2214	column="cy5_open_perimeter"
2215	channel="2"
2216	type="float"
2217	/>
2218	<property
2219	name="XCoord_Cy5"
2220	title="X coordinate cy5"
2221	description="X coordinate (in pixels) of grid circle corresponding to the spot."
2222	column="cy5_x"
2223	channel="2"
2224	type="float"
2225	/>
2226	<property
2227	name="YCoord_Cy5"
2228	title="Y coordinate cy5"
2229	description="Y coordinate (in pixels) of grid circle corresponding to the spot."
2230	column="cy5_y"
2231	channel="2"
2232	type="float"
2233	/>
2234	<property
2235	name="Diameter_Cy5"
2236	title="Diameter cy5"
2237	description="Diameter (in pixels) of grid circle corresponding to the spot."
2238	column="cy5_diameter"
2239	channel="2"
2240	type="int"
2241	/>
2242	<property
2243	name="PositionOffset_Cy5"
2244	title="Position offset cy5"
2245	description="Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2246	column="cy5_offset"
2247	channel="2"
2248	type="float"
2249	/>
2250	<property
2251	name="OffsetX_Cy5"
2252	title="X offset cy5"
2253	description="X Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2254	column="cy5_offset_x"
2255	channel="2"
2256	type="float"
2257	/>
2258	<property
2259	name="OffsetY_Cy5"
2260	title="Y offset cy5"
2261	description="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid."
2262	column="cy5_offset_y"
2263	channel="2"
2264	type="float"
2265	/>
2266	<property
2267	name="ExpectedX_Cy5"
2268	title="X expected cy5"
2269	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."
2270	column="cy5_x_expected"
2271	channel="2"
2272	type="float"
2273	/>
2274	<property
2275	name="ExpectedY_Cy5"
2276	title="Y expected cy5"
2277	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."
2278	column="cy5_y_expected"
2279	channel="2"
2280	type="float"
2281	/>
2282	<property
2283	name="CMX_Cy5"
2284	title="CM X coordinate cy5"
2285	description="X coordinate of the center of the mass of spot's signal region."
2286	column="cy5_x_cm"
2287	channel="2"
2288	type="float"
2289	/>
2290	<property
2291	name="CMY_Cy5"
2292	title="CM Y coordinate cy5"
2293	description="Y coordinate of the center of the mass of spot's signal region."
2294	column="cy5_y_cm"
2295	channel="2"
2296	type="float"
2297	/>
2298	<property
2299	name="CMOffset_Cy5"
2300	title="CM offset cy5"
2301	description="Offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2302	column="cy5_offset_cm"
2303	channel="2"
2304	type="float"
2305	/>
2306	<property
2307	name="CMOffsetX_Cy5"
2308	title="CM X offset cy5"
2309	description="X offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2310	column="cy5_offset_x_cm"
2311	channel="2"
2312	type="float"
2313	/>
2314	<property
2315	name="CMOffsetY_Cy5"
2316	title="CM Y offset cy5"
2317	description="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid."
2318	column="cy5_offset_y_cm"
2319	channel="2"
2320	type="float"
2321	/>
2322	<property
2323	name="MinDiam_Cy5"
2324	title="Min diameter cy5"
2325	description="Diameter of the circle inscribed into the spot's signal region."
2326	column="cy5_diameter_min"
2327	channel="2"
2328	type="float"
2329	/>
2330	<property
2331	name="MaxDiam_Cy5"
2332	title="Max diameter cy5"
2333	description="Diameter of the circle, the spot's signal region can be inscribed in."
2334	column="cy5_diameter_max"
2335	channel="2"
2336	type="float"
2337	/>
2338	<property
2339	name="Control_Cy5"
2340	title="Control cy5"
2341	description="Name of a control type for current spot (no name means the spot is not a control spot)."
2342	column="cy5_control"
2343	channel="2"
2344	type="string"
2345	/>
2346	<property
2347	name="FailedControl_Cy5"
2348	title="Failed control cy5"
2349	description="0 if the control passed all tests, 1 if at least one of the tests failed."
2350	column="cy5_control_failed"
2351	channel="2"
2352	type="boolean"
2353	/>
2354	<property
2355	name="BackgroundContaminationPresent_Cy5"
2356	title="Bg contamination cy5"
2357	description="0 if the spot passed background contamination test, 1 if it did not."
2358	column="cy5_bg_contamination"
2359	channel="2"
2360	type="boolean"
2361	/>
2362	<property
2363	name="SignalContaminationPresent_Cy5"
2364	title="Signal contamination cy5"
2365	description="0 if the spot passed signal contamination test, 1 if it did not."
2366	column="cy5_signal_contamination"
2367	channel="2"
2368	type="boolean"
2369	/>
2370	<property
2371	name="IgnoredFailed_Cy5"
2372	title="Ignored % failed cy5"
2373	description="0 if the spot passed ignored percentage test, 1 if it did not."
2374	column="cy5_ignored_failed"
2375	channel="2"
2376	type="boolean"
2377	/>
2378	<property
2379	name="OpenPerimeterFailed_Cy5"
2380	title="Open perimeter failed cy5"
2381	description="0 if the spot passed open perimeter test, 1 if it did not."
2382	column="cy5_perimeter_failed"
2383	channel="2"
2384	type="boolean"
2385	/>
2386	<property
2387	name="ShapeRegularityFailed_Cy5"
2388	title="Shape regularity failed cy5"
2389	description="0 if the spot passed shape regularity test, 1 if it did not."
2390	column="cy5_shape_failed"
2391	channel="2"
2392	type="boolean"
2393	/>
2394	<property
2395	name="PerimToAreaFailed_Cy5"
2396	title="Perimeter to area failed cy5"
2397	description="0 if the spot passed perimeter-to-area test, 1 if it did not."
2398	column="cy5_areapm_failed"
2399	channel="2"
2400	type="boolean"
2401	/>
2402	<property
2403	name="OffsetFailed_Cy5"
2404	title="Offset failed cy5"
2405	description="0 if the spot passed offset test, 1 if it did not."
2406	column="cy5_offset_failed"
2407	channel="2"
2408	type="boolean"
2409	/>
2410	<property
2411	name="EmptySpot_Cy5"
2412	title="Empty spot cy5"
2413	description="1 if the spot is empty, 0 if not."
2414	column="cy5_empty_spot"
2415	channel="2"
2416	type="boolean"
2417	/>
2418	<property
2419	name="NegativeSpot_Cy5"
2420	title="Negative spot cy5"
2421	description="1 if the spot was qualified as negative, 0 if it was not."
2422	column="cy5_negative_spot"
2423	channel="2"
2424	type="boolean"
2425	/>
2426	<property
2427	name="SelectedSpot_Cy5"
2428	title="Selected spot cy5"
2429	description="1 if the spot was selected in the software view at time of save, 0 if not."
2430	column="cy5_selected_spot"
2431	channel="2"
2432	type="boolean"
2433	/>
2434	<property
2435	name="SaturatedSpot_Cy5"
2436	title="Saturated spot cy5"
2437	description="1 if the spot was qualified as saturated, 0 if it was not."
2438	column="cy5_saturated_spot"
2439	channel="2"
2440	type="boolean"
2441	/>
2442	<intensity-formula
2443	name="mean"
2444	title="Mean FG - Mean BG"
2445	description="Subtract mean background from mean foreground"
2446	>
2447	<formula
2448	channel="1"
2449	expression="raw('SignalMean_Cy3') - raw('BackgroundMean_Cy3')"
2450	/>
2451	<formula
2452	channel="2"
2453	expression="raw('SignalMean_Cy5') - raw('BackgroundMean_Cy5')"
2454	/>
2455	</intensity-formula>
2456	<intensity-formula
2457	name="median"
2458	title="Median FG - Median BG"
2459	description="Subtract meadian background from median foreground"
2460	>
2461	<formula
2462	channel="1"
2463	expression="raw('SignalMedian_Cy3') - raw('BackgroundMedian_Cy3')"
2464	/>
2465	<formula
2466	channel="2"
2467	expression="raw('SignalMedian_Cy5') - raw('BackgroundMedian_Cy5')"
2468	/>
2469	</intensity-formula>
2470	<intensity-formula
2471	name="medianmean"
2472	title="Median FG - Mean BG"
2473	description="Subtract mean background from median foreground"
2474	>
2475	<formula
2476	channel="1"
2477	expression="raw('SignalMedian_Cy3') - raw('BackgroundMean_Cy3')"
2478	/>
2479	<formula
2480	channel="2"
2481	expression="raw('SignalMedian_Cy5') - raw('BackgroundMean_Cy5')"
2482	/>
2483	</intensity-formula>
2484	<intensity-formula
2485	name="meanmedian"
2486	title="Mean FG - Median BG"
2487	description="Subtract median background from mean foreground"
2488	>
2489	<formula
2490	channel="1"
2491	expression="raw('SignalMean_Cy3') - raw('BackgroundMedian_Cy3')"
2492	/>
2493	<formula
2494	channel="2"
2495	expression="raw('SignalMean_Cy5') - raw('BackgroundMedian_Cy5')"
2496	/>
2497	</intensity-formula>
2498	<intensity-formula
2499	name="meanfg"
2500	title="Mean FG"
2501	description="Mean foreground"
2502	>
2503	<formula
2504	channel="1"
2505	expression="raw('SignalMean_Cy3')"
2506	/>
2507	<formula
2508	channel="2"
2509	expression="raw('SignalMean_Cy5')"
2510	/>
2511	</intensity-formula>
2512	<intensity-formula
2513	name="medianfg"
2514	title="Median FG"
2515	description="Median foreground"
2516	>
2517	<formula
2518	channel="1"
2519	expression="raw('SignalMedian_Cy3')"
2520	/>
2521	<formula
2522	channel="2"
2523	expression="raw('SignalMedian_Cy5')"
2524	/>
2525	</intensity-formula>
2526	<intensity-formula
2527	name="medianfgmeanmedianbg"
2528	title="Median FG - Mean(Median BG)"
2529	description="Subtract mean of median backgrounds from median foreground"
2530	>
2531	<formula
2532	channel="1"
2533	expression="raw('SignalMedian_Cy3') - mean('BackgroundMedian_Cy3')"
2534	/>
2535	<formula
2536	channel="2"
2537	expression="raw('SignalMedian_Cy5') - mean('BackgroundMedian_Cy5')"
2538	/>
2539	</intensity-formula>
2540	<intensity-formula
2541	name="meanfgmeanmeanbg"
2542	title="Mean FG - Mean(Mean BG)"
2543	description="Subtract mean of mean backgrounds from mean foreground"
2544	>
2545	<formula
2546	channel="1"
2547	expression="raw('SignalMean_Cy3') - mean('BackgroundMean_Cy3')"
2548	/>
2549	<formula
2550	channel="2"
2551	expression="raw('SignalMean_Cy5') - mean('BackgroundMean_Cy5')"
2552	/>
2553	</intensity-formula>
2554	<intensity-formula
2555	name="medianfgmeanmeanbg"
2556	title="Median FG - Mean(Mean BG)"
2557	description="Subtract mean of mean backgrounds from median foreground"
2558	>
2559	<formula
2560	channel="1"
2561	expression="raw('SignalMedian_Cy3') - mean('BackgroundMean_Cy3')"
2562	/>
2563	<formula
2564	channel="2"
2565	expression="raw('SignalMedian_Cy5') - mean('BackgroundMean_Cy5')"
2566	/>
2567	</intensity-formula>
2568	<intensity-formula
2569	name="meanfgmeanmedianbg"
2570	title="Mean FG - Mean(Median BG)"
2571	description="Subtract mean of median backgrounds from mean foreground"
2572	>
2573	<formula
2574	channel="1"
2575	expression="raw('SignalMean_Cy3') - mean('BackgroundMedian_Cy3')"
2576	/>
2577	<formula
2578	channel="2"
2579	expression="raw('SignalMean_Cy5') - mean('BackgroundMedian_Cy5')"
2580	/>
2581	</intensity-formula>
2582	</raw-data-type>
2583
2584	<raw-data-type
2585	id="quantarraybiotin"
2586	channels="1"
2587	name="QuantArray Biotin"
2588	table="RawDataQuantArrayBiotin"
2589	>
2590	<property
2591	name="Number"
2592	title="Number"
2593	description="Number."
2594	column="number"
2595	type="int"
2596	/>
2597	<property
2598	name="BiotinIntensity"
2599	title="Intensity"
2600	description="Mean pixel biotin foreground intensity in biotin channel."
2601	column="intensity"
2602	channel="1"
2603	type="float"
2604	/>
2605	<property
2606	name="BiotinBackground"
2607	title="Background"
2608	description="Mean pixel biotin background intensity in biotin channel."
2609	column="background"
2610	channel="1"
2611	type="float"
2612	/>
2613	<property
2614	name="BiotinDiameter"
2615	title="Diameter"
2616	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."
2617	column="diameter"
2618	channel="1"
2619	type="float"
2620	/>
2621	<property
2622	name="BiotinArea"
2623	title="Area"
2624	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."
2625	column="area"
2626	channel="1"
2627	type="int"
2628	/>
2629	<property
2630	name="BiotinFootprint"
2631	title="Footprint"
2632	description="The distance between the expected position of a spot and its actual measured position (in microns)."
2633	column="footprint"
2634	channel="1"
2635	type="float"
2636	/>
2637	<property
2638	name="BiotinCircularity"
2639	title="Circularity"
2640	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."
2641	column="cirularity"
2642	channel="1"
2643	type="float"
2644	/>
2645	<property
2646	name="BiotinSpotUniformity"
2647	title="Spot uniformity"
2648	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."
2649	column="uniformity"
2650	channel="1"
2651	type="float"
2652	/>
2653	<property
2654	name="BiotinBkgUniformity"
2655	title="Background uniformity"
2656	description="The uniformity of the pixels used in the background intensity calculation."
2657	column="bg_uniformity"
2658	channel="1"
2659	type="float"
2660	/>
2661	<property
2662	name="BiotinSignalNoiseRatio"
2663	title="Signal noise ratio"
2664	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."
2665	column="snr"
2666	channel="1"
2667	type="float"
2668	/>
2669	<property
2670	name="BiotinConfidence"
2671	title="Confidence"
2672	description="Confidence."
2673	column="confidence"
2674	channel="1"
2675	type="int"
2676	/>
2677	<property
2678	name="IgnoreFilter"
2679	title="Ignore filter"
2680	description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2681	column="ignore_filter"
2682	type="int"
2683	/>
2684	<property
2685	name="BiotinRatio"
2686	title="Ratio"
2687	description="The portion of the overall spot fluorescence contributed by biotin channel (normalized so that biotin channel contribution equals 1)."
2688	column="ratio"
2689	channel="1"
2690	type="int"
2691	/>
2692	<property
2693	name="BiotinPercent"
2694	title="Percent"
2695	description="The portion of the overall spot fluorescence contributed by biotin channel (in percent)."
2696	column="precent"
2697	channel="1"
2698	type="float"
2699	/>
2700	<property
2701	name="BiotinDiameterFilter"
2702	title="Diameter filter"
2703	description="Biotin diameter filter."
2704	column="diameter_filter"
2705	type="int"
2706	/>
2707	<property
2708	name="BiotinAreaFilter"
2709	title="Area filter"
2710	description="Biotin area filter."
2711	column="area_filter"
2712	type="int"
2713	/>
2714	<property
2715	name="BiotinFootprintFilter"
2716	title="Footprint filter"
2717	description="Biotin footprint filter."
2718	column="footprint_filter"
2719	type="int"
2720	/>
2721	<property
2722	name="BiotinCircularityFilter"
2723	title="Circularity filter"
2724	description="Biotin circularity filter."
2725	column="circularity_filter"
2726	type="int"
2727	/>
2728	<property
2729	name="BiotinSpotUniformityFilter"
2730	title="Spot uniformity filter"
2731	description="Biotin spot uniformity filter."
2732	column="uniformity_filter"
2733	type="int"
2734	/>
2735	<property
2736	name="BiotinBkgUniformityFilter"
2737	title="Background uniformity filter"
2738	description="Biotin background uniformity filter."
2739	column="bg_uniformity_filter"
2740	type="int"
2741	/>
2742	<property
2743	name="BiotinSignalNoiseRatioFilter"
2744	title="Signal noise ratio filter"
2745	description="Biotin signal noise ratio filter."
2746	column="snr_filter"
2747	type="int"
2748	/>
2749	<property
2750	name="BiotinReplicateFilter"
2751	title="Replicate filter"
2752	description="Biotin replicate filter."
2753	column="replicate_filter"
2754	type="int"
2755	/>
2756	<intensity-formula
2757	name="meanfg"
2758	title="Mean FG"
2759	description="Mean foreground intensity"
2760	>
2761	<formula
2762	channel="1"
2763	expression="raw('intensity')"
2764	/>
2765	</intensity-formula>
2766	<intensity-formula
2767	name="mean"
2768	title="Mean FG - Mean BG"
2769	description="Subtract mean background from mean foreground"
2770	>
2771	<formula
2772	channel="1"
2773	expression="raw('BiotinIntensity') - raw('BiotinBackground')"
2774	/>
2775	</intensity-formula>
2776	</raw-data-type>
2777
2778	<raw-data-type
2779	id="quantarraycy"
2780	channels="2"
2781	name="QuantArray Cy"
2782	table="RawDataQuantArrayCy"
2783	>
2784	<property
2785	name="Cy3Intensity"
2786	title="Mean Cy3 intensity"
2787	description="Mean pixel Cy3 foreground intensity in Channel Cy3."
2788	column="cy3_mean"
2789	channel="1"
2790	type="float"
2791	/>
2792	<property
2793	name="Cy3Background"
2794	title="Mean Cy3 background"
2795	description="Mean pixel Cy3 background intensity in Channel Cy3."
2796	column="cy3_mean_bg"
2797	channel="1"
2798	type="float"
2799	/>
2800	<property
2801	name="Cy3Diameter"
2802	title="Cy3 spot diameter"
2803	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."
2804	column="cy3_diameter"
2805	channel="1"
2806	type="float"
2807	/>
2808	<property
2809	name="Cy3Area"
2810	title="Cy3 spot area"
2811	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."
2812	column="cy3_area"
2813	channel="1"
2814	type="int"
2815	/>
2816	<property
2817	name="Cy3Footprint"
2818	title="Cy3 footprint"
2819	description="The distance between the expected position of a spot and its actual measured position (in microns)."
2820	column="cy3_footprint"
2821	channel="1"
2822	type="float"
2823	/>
2824	<property
2825	name="Cy3Circularity"
2826	title="Cy3 circularity"
2827	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."
2828	column="cy3_circularity"
2829	channel="1"
2830	type="float"
2831	/>
2832	<property
2833	name="Cy3SpotUniformity"
2834	title="Cy3 spot uniformity"
2835	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."
2836	column="cy3_uniformity"
2837	channel="1"
2838	type="float"
2839	/>
2840	<property
2841	name="Cy3BkgUniformity"
2842	title="Cy3 background uniformity"
2843	description="The uniformity of the pixels used in the background intensity calculation."
2844	column="cy3_bg_uniformity"
2845	channel="1"
2846	type="float"
2847	/>
2848	<property
2849	name="Cy3SignalNoiseRatio"
2850	title="Cy3 signal noise ratio"
2851	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."
2852	column="cy3_snr"
2853	channel="1"
2854	type="float"
2855	/>
2856	<property
2857	name="Cy3Confidence"
2858	title="Cy3 confidence"
2859	description="Unused QuantArray feature, will always = 1."
2860	column="cy3_confidence"
2861	channel="2"
2862	type="int"
2863	/>
2864	<property
2865	name="Cy5Intensity"
2866	title="Mean Cy5 intensity"
2867	description="Mean pixel Cy5 foreground intensity in Channel Cy5."
2868	column="cy5_mean"
2869	channel="2"
2870	type="float"
2871	/>
2872	<property
2873	name="Cy5Background"
2874	title="Mean Cy5 background"
2875	description="Mean pixel Cy5 background intensity in Channel Cy5."
2876	column="cy5_mean_bg"
2877	channel="2"
2878	type="float"
2879	/>
2880	<property
2881	name="Cy5Diameter"
2882	title="Cy5 spot diameter"
2883	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."
2884	column="cy5_diameter"
2885	channel="2"
2886	type="float"
2887	/>
2888	<property
2889	name="Cy5Area"
2890	title="Cy5 spot area"
2891	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."
2892	column="cy5_area"
2893	channel="2"
2894	type="int"
2895	/>
2896	<property
2897	name="Cy5Footprint"
2898	title="Cy5 footprint"
2899	description="The distance between the expected position of a spot and its actual measured position (in microns)."
2900	column="cy5_footprint"
2901	channel="2"
2902	type="float"
2903	/>
2904	<property
2905	name="Cy5Circularity"
2906	title="Cy5 circularity"
2907	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."
2908	column="cy5_circularity"
2909	channel="2"
2910	type="float"
2911	/>
2912	<property
2913	name="Cy5SpotUniformity"
2914	title="Cy5 spot uniformity"
2915	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."
2916	column="cy5_uniformity"
2917	channel="2"
2918	type="float"
2919	/>
2920	<property
2921	name="Cy5BkgUniformity"
2922	title="Cy5 background uniformity"
2923	description="The uniformity of the pixels used in the background intensity calculation."
2924	column="cy5_bg_uniformity"
2925	channel="2"
2926	type="float"
2927	/>
2928	<property
2929	name="Cy5SignalNoiseRatio"
2930	title="Cy5 signal noise ratio"
2931	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."
2932	column="cy5_snr"
2933	channel="2"
2934	type="float"
2935	/>
2936	<property
2937	name="Cy5Confidence"
2938	title="Cy5 confidence"
2939	description="Unused QuantArray feature, will always = 1."
2940	column="cy5_confidence"
2941	channel="2"
2942	type="int"
2943	/>
2944	<property
2945	name="IgnoreFilter"
2946	title="Ignore filter"
2947	description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
2948	column="ignore_filter"
2949	type="int"
2950	/>
2951	<property
2952	name="Cy3Ratio"
2953	title="Cy3 ratio"
2954	description="The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1)."
2955	column="cy3_ratio"
2956	channel="1"
2957	type="float"
2958	/>
2959	<property
2960	name="Cy3Percent"
2961	title="Cy3 precent"
2962	description="The portion of the overall spot fluorescence contributed by channel Cy3 (in percent)."
2963	column="cy3_percent"
2964	channel="1"
2965	type="float"
2966	/>
2967	<property
2968	name="Cy3SignalNoiseRatioFilter"
2969	title="Cy3 signal noise ratio filter"
2970	description="Cy3 signal noise ratio filter"
2971	column="cy3_snr_filter"
2972	channel="1"
2973	type="float"
2974	/>
2975	<property
2976	name="Cy5Ratio"
2977	title="Cy5 ratio"
2978	description="The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1)."
2979	column="cy5_ratio"
2980	channel="2"
2981	type="float"
2982	/>
2983	<property
2984	name="Cy5Percent"
2985	title="Cy5 precent"
2986	description="The portion of the overall spot fluorescence contributed by channel Cy5 (in percent)."
2987	column="cy5_percent"
2988	channel="2"
2989	type="float"
2990	/>
2991	<property
2992	name="Cy5SignalNoiseRatioFilter"
2993	title="Cy5 signal noise ratio filter"
2994	description="Cy5 signal noise ratio filter"
2995	column="cy5_snr_filter"
2996	channel="2"
2997	type="float"
2998	/>
2999	<property
3000	name="log_normalised"
3001	title="Normalized ratio"
3002	description="Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1"
3003	column="log_normalised"
3004	type="float"
3005	/>
3006	<intensity-formula
3007	name="meanfg"
3008	title="Mean FG"
3009	description="Mean foreground intensity"
3010	>
3011	<formula
3012	channel="1"
3013	expression="raw('Cy3Intensity')"
3014	/>
3015	<formula
3016	channel="2"
3017	expression="raw('Cy5Intensity')"
3018	/>
3019	</intensity-formula>
3020	<intensity-formula
3021	name="mean"
3022	title="Mean FG - Mean BG"
3023	description="Subtract mean background from mean foreground"
3024	>
3025	<formula
3026	channel="1"
3027	expression="raw('Cy3Intensity') - raw('Cy3Background')"
3028	/>
3029	<formula
3030	channel="2"
3031	expression="raw('Cy5Intensity') - raw('Cy5Background')"
3032	/>
3033	</intensity-formula>
3034	</raw-data-type>
3035
3036	<raw-data-type
3037	id="spotfinder"
3038	channels="2"
3039	name="Spotfinder"
3040	table="RawDataSpotfinder"
3041	>
3042	<property
3043	name="intA"
3044	title="Intensity A"
3045	description="Spot intensity in channel A corrected for background."
3046	column="int_a"
3047	type="int"
3048	channel="1"
3049	/>
3050	<property
3051	name="intB"
3052	title="Intensity B"
3053	description="Spot intensity in channel B corrected for background."
3054	column="int_b"
3055	type="int"
3056	channel="2"
3057	/>
3058	<property
3059	name="meanRatio"
3060	title="Mean ratio"
3061	description="Spot mean ratio."
3062	column="mean_ratio"
3063	type="float"
3064	/>
3065	<property
3066	name="area"
3067	title="Area"
3068	description="Spot total area in pixels."
3069	column="area"
3070	type="int"
3071	/>
3072	<property
3073	name="saturation"
3074	title="Saturation factor"
3075	description="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration."
3076	column="saturation"
3077	type="float"
3078	/>
3079	<property
3080	name="medianRatio"
3081	title="Median ratio"
3082	description="Spot median ratio."
3083	column="median_ratio"
3084	type="float"
3085	/>
3086	<property
3087	name="modeRatio"
3088	title="Mode ratio"
3089	description="Spot mode ratio."
3090	column="mode_ratio"
3091	type="float"
3092	/>
3093	<property
3094	name="bgA"
3095	title="Background A"
3096	description="Spot background in channel A."
3097	column="bg_a"
3098	channel="1"
3099	type="int"
3100	/>
3101	<property
3102	name="bgB"
3103	title="Background B"
3104	description="Spot background in channel B."
3105	column="bg_b"
3106	channel="2"
3107	type="int"
3108	/>
3109	<property
3110	name="flagA"
3111	title="Flag A"
3112	description="Spot flag in channel A. This flag is set by QC filter."
3113	column="flag_a"
3114	channel="1"
3115	type="string"
3116	/>
3117	<property
3118	name="flagB"
3119	title="Flag B"
3120	description="Spot flag in channel B. This flag is set by QC filter."
3121	column="flag_b"
3122	channel="2"
3123	type="string"
3124	/>
3125	<property
3126	name="qcA"
3127	title="Spot QC score A"
3128	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."
3129	column="qc_a"
3130	channel="1"
3131	type="float"
3132	/>
3133	<property
3134	name="qcB"
3135	title="Spot QC score B"
3136	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."
3137	column="qc_b"
3138	channel="2"
3139	type="float"
3140	/>
3141	<property
3142	name="qcTotal"
3143	title="Total QC"
3144	description="Spot total QC score. This is a mean of QC scores in channels A and B."
3145	column="qc_total"
3146	type="float"
3147	/>
3148	<property
3149	name="flag"
3150	title="Flag"
3151	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."
3152	column="flag"
3153	type="string"
3154	/>
3155	<intensity-formula
3156	name="int"
3157	title="Spot intensity"
3158	description="Spot intensity corrected for background."
3159	>
3160	<formula
3161	channel="1"
3162	expression="raw('intA')"
3163	/>
3164	<formula
3165	channel="2"
3166	expression="raw('intB')"
3167	/>
3168	</intensity-formula>
3169	</raw-data-type>
3170	</raw-data-types>
3171

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