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source: trunk/config/dist/raw-data-types.xml @ 2959

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

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