source: trunk/misc/mage/rawdatatypes/QT_Agilent.xml @ 1938

Last change on this file since 1938 was 1938, checked in by Nicklas Nordborg, 17 years ago

Added QuantArray? raw data types
Added some intensity formulas to other raw data types
Added MAGE files describing raw data types
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 55.0 KB
Line 
1<?xml version="1.0" encoding="UTF-8" standalone="no"?>
2<?xml-stylesheet type="text/xsl" href="QT.xsl"?>
3<!DOCTYPE MAGE-ML PUBLIC "-//OMG//DTD MAGE-ML 1.0//EN" "http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd">
4<MAGE-ML identifier="Agilent.BRS:MAGE-ML:1">
5  <Descriptions_assnlist>
6    <Description>
7      <Annotations_assnlist>
8  <OntologyEntry category="Software" value="Agilent Feature Extraction Software" description="Version A.7.5.1; Jun 1 2004 09:45:12"/>
9      </Annotations_assnlist>
10    </Description>
11  </Descriptions_assnlist>
12  <QuantitationType_package>
13    <QuantitationType_assnlist>
14      <SpecializedQuantitationType name="PositionX" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:PositionX" isBackground="false">
15  <Descriptions_assnlist>
16    <Description text="Found X coordinate of the feature centroid currently reported in pixels."/>
17  </Descriptions_assnlist>
18  <Scale_assn>
19    <OntologyEntry value="linear_scale" category="Scale"/>
20  </Scale_assn>
21  <DataType_assn>
22    <OntologyEntry value="float" category="DataType"/>
23  </DataType_assn>
24      </SpecializedQuantitationType>
25      <SpecializedQuantitationType name="PositionY" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:PositionY" isBackground="false">
26  <Descriptions_assnlist>
27    <Description text="Found Y coordinate of the feature centroid currently reported in pixels."/>
28  </Descriptions_assnlist>
29  <Scale_assn>
30    <OntologyEntry value="linear_scale" category="Scale"/>
31  </Scale_assn>
32  <DataType_assn>
33    <OntologyEntry value="float" category="DataType"/>
34  </DataType_assn>
35      </SpecializedQuantitationType>
36      <Ratio name="LogRatio" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:LogRatio" isBackground="false">
37  <Descriptions_assnlist>
38    <Description text="log(REDsignal/GREENsignal) per feature. Signals in both channels are post dye normalization. If SURROGATES are disabled, then this value will be set to: -2 if DyeNormRedSig &lt;= 0.0 &amp;DyeNormGreenSig > 0.0; 2 if DyeNormRedSig > 0.0 &amp; DyeNormGreenSig &lt;= 0.0; and 0 if DyeNormRedSig &lt;= 0.0 &amp; DyeNormGreenSig &lt;= 0.0."/>
39  </Descriptions_assnlist>
40  <Scale_assn>
41    <OntologyEntry value="log_base_10" category="Scale"/>
42  </Scale_assn>
43  <DataType_assn>
44    <OntologyEntry value="float" category="DataType"/>
45  </DataType_assn>
46      </Ratio>
47      <Error name="LogRatioError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:LogRatioError" isBackground="false">
48  <Descriptions_assnlist>
49    <Description text="LogRatioError = error of the log ratio calculated according to the error model chosen. If SURROGATES are disabled, then this value will be set to if DyeNormRedSig &lt;= 0.0 OR DyeNormGreenSig &lt;= 0.0."/>
50  </Descriptions_assnlist>
51  <Scale_assn>
52    <OntologyEntry value="log_base_10" category="Scale"/>
53  </Scale_assn>
54  <DataType_assn>
55    <OntologyEntry value="float" category="DataType"/>
56  </DataType_assn>
57  <TargetQuantitationType_assnref>
58    <Ratio_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:LogRatio"/>
59  </TargetQuantitationType_assnref>
60      </Error>
61      <PValue name="PValueLogRatio" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:PValueLogRatio" isBackground="false">
62  <Descriptions_assnlist>
63    <Description text="Significance level of the Log Ratio computed for a feature."/>
64  </Descriptions_assnlist>
65  <Scale_assn>
66    <OntologyEntry value="percent" category="Scale"/>
67  </Scale_assn>
68  <DataType_assn>
69    <OntologyEntry value="float" category="DataType"/>
70  </DataType_assn>
71  <TargetQuantitationType_assnref>
72    <Ratio_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:LogRatio"/>
73  </TargetQuantitationType_assnref>
74      </PValue>
75      <SpecializedQuantitationType name="gSurrogateUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gSurrogateUsed" isBackground="false">
76  <Descriptions_assnlist>
77    <Description text="The green surrogate value used."/>
78  </Descriptions_assnlist>
79  <Channel_assnref>
80    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
81  </Channel_assnref>
82  <Scale_assn>
83    <OntologyEntry value="linear_scale" category="Scale"/>
84  </Scale_assn>
85  <DataType_assn>
86    <OntologyEntry value="float" category="DataType"/>
87  </DataType_assn>
88      </SpecializedQuantitationType>
89      <SpecializedQuantitationType name="rSurrogateUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rSurrogateUsed" isBackground="false">
90  <Descriptions_assnlist>
91    <Description text="The red surrogate value used."/>
92  </Descriptions_assnlist>
93  <Channel_assnref>
94    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
95  </Channel_assnref>
96  <Scale_assn>
97    <OntologyEntry value="linear_scale" category="Scale"/>
98  </Scale_assn>
99  <DataType_assn>
100    <OntologyEntry value="float" category="DataType"/>
101  </DataType_assn>
102      </SpecializedQuantitationType>
103      <SpecializedQuantitationType name="gIsFound" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsFound" isBackground="false">
104  <Descriptions_assnlist>
105    <Description text="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."/>
106  </Descriptions_assnlist>
107  <Channel_assnref>
108    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
109  </Channel_assnref>
110  <Scale_assn>
111    <OntologyEntry value="linear_scale" category="Scale"/>
112  </Scale_assn>
113  <DataType_assn>
114    <OntologyEntry value="boolean" category="DataType"/>
115  </DataType_assn>
116      </SpecializedQuantitationType>
117      <SpecializedQuantitationType name="rIsFound" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsFound" isBackground="false">
118  <Descriptions_assnlist>
119    <Description text="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."/>
120  </Descriptions_assnlist>
121  <Channel_assnref>
122    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
123  </Channel_assnref>
124  <Scale_assn>
125    <OntologyEntry value="linear_scale" category="Scale"/>
126  </Scale_assn>
127  <DataType_assn>
128    <OntologyEntry value="boolean" category="DataType"/>
129  </DataType_assn>
130      </SpecializedQuantitationType>
131      <DerivedSignal name="gProcessedSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gProcessedSignal" isBackground="false">
132  <Descriptions_assnlist>
133    <Description text="The propagated feature signal, per channel, used for computation of log ratio."/>
134  </Descriptions_assnlist>
135  <Channel_assnref>
136    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
137  </Channel_assnref>
138  <Scale_assn>
139    <OntologyEntry value="linear_scale" category="Scale"/>
140  </Scale_assn>
141  <DataType_assn>
142    <OntologyEntry value="float" category="DataType"/>
143  </DataType_assn>
144      </DerivedSignal>
145      <DerivedSignal name="rProcessedSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rProcessedSignal" isBackground="false">
146  <Descriptions_assnlist>
147    <Description text="The propagated feature signal, per channel, used for computation of log ratio."/>
148  </Descriptions_assnlist>
149  <Channel_assnref>
150    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
151  </Channel_assnref>
152  <Scale_assn>
153    <OntologyEntry value="linear_scale" category="Scale"/>
154  </Scale_assn>
155  <DataType_assn>
156    <OntologyEntry value="float" category="DataType"/>
157  </DataType_assn>
158      </DerivedSignal>
159      <Error name="gProcessedSigError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gProcessedSigError" isBackground="false">
160  <Descriptions_assnlist>
161    <Description text="Standard error of propagated feature signal, per channel."/>
162  </Descriptions_assnlist>
163  <Channel_assnref>
164    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
165  </Channel_assnref>
166  <Scale_assn>
167    <OntologyEntry value="linear_scale" category="Scale"/>
168  </Scale_assn>
169  <DataType_assn>
170    <OntologyEntry value="float" category="DataType"/>
171  </DataType_assn>
172  <TargetQuantitationType_assnref>
173    <DerivedSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gProcessedSignal"/>
174  </TargetQuantitationType_assnref>
175      </Error>
176      <Error name="rProcessedSigError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rProcessedSigError" isBackground="false">
177  <Descriptions_assnlist>
178    <Description text="Standard error of propagated feature signal, per channel."/>
179  </Descriptions_assnlist>
180  <Channel_assnref>
181    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
182  </Channel_assnref>
183  <Scale_assn>
184    <OntologyEntry value="linear_scale" category="Scale"/>
185  </Scale_assn>
186  <DataType_assn>
187    <OntologyEntry value="float" category="DataType"/>
188  </DataType_assn>
189  <TargetQuantitationType_assnref>
190    <DerivedSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rProcessedSignal"/>
191  </TargetQuantitationType_assnref>
192      </Error>
193      <SpecializedQuantitationType name="gNumPixOLHi" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gNumPixOLHi" isBackground="false">
194  <Descriptions_assnlist>
195    <Description text="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."/>
196  </Descriptions_assnlist>
197  <Channel_assnref>
198    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
199  </Channel_assnref>
200  <Scale_assn>
201    <OntologyEntry value="linear_scale" category="Scale"/>
202  </Scale_assn>
203  <DataType_assn>
204    <OntologyEntry value="integer" category="DataType"/>
205  </DataType_assn>
206      </SpecializedQuantitationType>
207      <SpecializedQuantitationType name="rNumPixOLHi" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rNumPixOLHi" isBackground="false">
208  <Descriptions_assnlist>
209    <Description text="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."/>
210  </Descriptions_assnlist>
211  <Channel_assnref>
212    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
213  </Channel_assnref>
214  <Scale_assn>
215    <OntologyEntry value="linear_scale" category="Scale"/>
216  </Scale_assn>
217  <DataType_assn>
218    <OntologyEntry value="integer" category="DataType"/>
219  </DataType_assn>
220      </SpecializedQuantitationType>
221      <SpecializedQuantitationType name="gNumPixOLLo" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gNumPixOLLo" isBackground="false">
222  <Descriptions_assnlist>
223    <Description text="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."/>
224  </Descriptions_assnlist>
225  <Channel_assnref>
226    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
227  </Channel_assnref>
228  <Scale_assn>
229    <OntologyEntry value="linear_scale" category="Scale"/>
230  </Scale_assn>
231  <DataType_assn>
232    <OntologyEntry value="integer" category="DataType"/>
233  </DataType_assn>
234      </SpecializedQuantitationType>
235      <SpecializedQuantitationType name="rNumPixOLLo" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rNumPixOLLo" isBackground="false">
236  <Descriptions_assnlist>
237    <Description text="Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction."/>
238  </Descriptions_assnlist>
239  <Channel_assnref>
240    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
241  </Channel_assnref>
242  <Scale_assn>
243    <OntologyEntry value="linear_scale" category="Scale"/>
244  </Scale_assn>
245  <DataType_assn>
246    <OntologyEntry value="integer" category="DataType"/>
247  </DataType_assn>
248      </SpecializedQuantitationType>
249      <SpecializedQuantitationType name="gNumPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gNumPix" isBackground="false">
250  <Descriptions_assnlist>
251    <Description text="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."/>
252  </Descriptions_assnlist>
253  <Channel_assnref>
254    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
255  </Channel_assnref>
256  <Scale_assn>
257    <OntologyEntry value="linear_scale" category="Scale"/>
258  </Scale_assn>
259  <DataType_assn>
260    <OntologyEntry value="integer" category="DataType"/>
261  </DataType_assn>
262      </SpecializedQuantitationType>
263      <SpecializedQuantitationType name="rNumPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rNumPix" isBackground="false">
264  <Descriptions_assnlist>
265    <Description text="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."/>
266  </Descriptions_assnlist>
267  <Channel_assnref>
268    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
269  </Channel_assnref>
270  <Scale_assn>
271    <OntologyEntry value="linear_scale" category="Scale"/>
272  </Scale_assn>
273  <DataType_assn>
274    <OntologyEntry value="integer" category="DataType"/>
275  </DataType_assn>
276      </SpecializedQuantitationType>
277      <MeasuredSignal name="gMeanSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gMeanSignal" isBackground="false">
278  <Descriptions_assnlist>
279    <Description text="Raw mean signal of feature in green channel."/>
280  </Descriptions_assnlist>
281  <Channel_assnref>
282    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
283  </Channel_assnref>
284  <Scale_assn>
285    <OntologyEntry value="linear_scale" category="Scale"/>
286  </Scale_assn>
287  <DataType_assn>
288    <OntologyEntry value="float" category="DataType"/>
289  </DataType_assn>
290      </MeasuredSignal>
291      <MeasuredSignal name="rMeanSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rMeanSignal" isBackground="false">
292  <Descriptions_assnlist>
293    <Description text="Raw mean signal of feature in red channel."/>
294  </Descriptions_assnlist>
295  <Channel_assnref>
296    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
297  </Channel_assnref>
298  <Scale_assn>
299    <OntologyEntry value="linear_scale" category="Scale"/>
300  </Scale_assn>
301  <DataType_assn>
302    <OntologyEntry value="float" category="DataType"/>
303  </DataType_assn>
304      </MeasuredSignal>
305      <SpecializedQuantitationType name="gMedianSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gMedianSignal" isBackground="false">
306  <Descriptions_assnlist>
307    <Description text="Raw median signal of feature in green channel."/>
308  </Descriptions_assnlist>
309  <Channel_assnref>
310    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
311  </Channel_assnref>
312  <Scale_assn>
313    <OntologyEntry value="linear_scale" category="Scale"/>
314  </Scale_assn>
315  <DataType_assn>
316    <OntologyEntry value="float" category="DataType"/>
317  </DataType_assn>
318      </SpecializedQuantitationType>
319      <SpecializedQuantitationType name="rMedianSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rMedianSignal" isBackground="false">
320  <Descriptions_assnlist>
321    <Description text="Raw median signal of feature in red channel."/>
322  </Descriptions_assnlist>
323  <Channel_assnref>
324    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
325  </Channel_assnref>
326  <Scale_assn>
327    <OntologyEntry value="linear_scale" category="Scale"/>
328  </Scale_assn>
329  <DataType_assn>
330    <OntologyEntry value="float" category="DataType"/>
331  </DataType_assn>
332      </SpecializedQuantitationType>
333      <Error name="gPixSDev" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gPixSDev" isBackground="false">
334  <Descriptions_assnlist>
335    <Description text="Standard deviation of all inlier pixels per feature; this is computed independently in each channel."/>
336  </Descriptions_assnlist>
337  <Channel_assnref>
338    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
339  </Channel_assnref>
340  <Scale_assn>
341    <OntologyEntry value="linear_scale" category="Scale"/>
342  </Scale_assn>
343  <DataType_assn>
344    <OntologyEntry value="float" category="DataType"/>
345  </DataType_assn>
346  <TargetQuantitationType_assnref>
347    <MeasuredSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gMeanSignal"/>
348  </TargetQuantitationType_assnref>
349      </Error>
350      <Error name="rPixSDev" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rPixSDev" isBackground="false">
351  <Descriptions_assnlist>
352    <Description text="Standard deviation of all inlier pixels per feature; this is computed independently in each channel."/>
353  </Descriptions_assnlist>
354  <Channel_assnref>
355    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
356  </Channel_assnref>
357  <Scale_assn>
358    <OntologyEntry value="linear_scale" category="Scale"/>
359  </Scale_assn>
360  <DataType_assn>
361    <OntologyEntry value="float" category="DataType"/>
362  </DataType_assn>
363  <TargetQuantitationType_assnref>
364    <MeasuredSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rMeanSignal"/>
365  </TargetQuantitationType_assnref>
366      </Error>
367      <SpecializedQuantitationType name="gBGNumPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGNumPix" isBackground="false">
368  <Descriptions_assnlist>
369    <Description text="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."/>
370  </Descriptions_assnlist>
371  <Channel_assnref>
372    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
373  </Channel_assnref>
374  <Scale_assn>
375    <OntologyEntry value="linear_scale" category="Scale"/>
376  </Scale_assn>
377  <DataType_assn>
378    <OntologyEntry value="integer" category="DataType"/>
379  </DataType_assn>
380      </SpecializedQuantitationType>
381      <SpecializedQuantitationType name="rBGNumPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGNumPix" isBackground="false">
382  <Descriptions_assnlist>
383    <Description text="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."/>
384  </Descriptions_assnlist>
385  <Channel_assnref>
386    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
387  </Channel_assnref>
388  <Scale_assn>
389    <OntologyEntry value="linear_scale" category="Scale"/>
390  </Scale_assn>
391  <DataType_assn>
392    <OntologyEntry value="integer" category="DataType"/>
393  </DataType_assn>
394      </SpecializedQuantitationType>
395      <MeasuredSignal name="gBGMeanSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGMeanSignal" isBackground="true">
396  <Descriptions_assnlist>
397    <Description text="Mean local background signal (local to corresponding feature) computed per channel."/>
398  </Descriptions_assnlist>
399  <Channel_assnref>
400    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
401  </Channel_assnref>
402  <Scale_assn>
403    <OntologyEntry value="linear_scale" category="Scale"/>
404  </Scale_assn>
405  <DataType_assn>
406    <OntologyEntry value="float" category="DataType"/>
407  </DataType_assn>
408      </MeasuredSignal>
409      <MeasuredSignal name="rBGMeanSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGMeanSignal" isBackground="true">
410  <Descriptions_assnlist>
411    <Description text="Mean local background signal (local to corresponding feature) computed per channel."/>
412  </Descriptions_assnlist>
413  <Channel_assnref>
414    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
415  </Channel_assnref>
416  <Scale_assn>
417    <OntologyEntry value="linear_scale" category="Scale"/>
418  </Scale_assn>
419  <DataType_assn>
420    <OntologyEntry value="float" category="DataType"/>
421  </DataType_assn>
422      </MeasuredSignal>
423      <SpecializedQuantitationType name="gBGMedianSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGMedianSignal" isBackground="true">
424  <Descriptions_assnlist>
425    <Description text="Median local background signal (local to corresponding feature) computed per channel."/>
426  </Descriptions_assnlist>
427  <Channel_assnref>
428    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
429  </Channel_assnref>
430  <Scale_assn>
431    <OntologyEntry value="linear_scale" category="Scale"/>
432  </Scale_assn>
433  <DataType_assn>
434    <OntologyEntry value="float" category="DataType"/>
435  </DataType_assn>
436      </SpecializedQuantitationType>
437      <SpecializedQuantitationType name="rBGMedianSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGMedianSignal" isBackground="true">
438  <Descriptions_assnlist>
439    <Description text="Median local background signal (local to corresponding feature) computed per channel."/>
440  </Descriptions_assnlist>
441  <Channel_assnref>
442    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
443  </Channel_assnref>
444  <Scale_assn>
445    <OntologyEntry value="linear_scale" category="Scale"/>
446  </Scale_assn>
447  <DataType_assn>
448    <OntologyEntry value="float" category="DataType"/>
449  </DataType_assn>
450      </SpecializedQuantitationType>
451      <Error name="gBGPixSDev" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGPixSDev" isBackground="true">
452  <Descriptions_assnlist>
453    <Description text="Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel."/>
454  </Descriptions_assnlist>
455  <Channel_assnref>
456    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
457  </Channel_assnref>
458  <Scale_assn>
459    <OntologyEntry value="linear_scale" category="Scale"/>
460  </Scale_assn>
461  <DataType_assn>
462    <OntologyEntry value="float" category="DataType"/>
463  </DataType_assn>
464  <TargetQuantitationType_assnref>
465    <MeasuredSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGMeanSignal"/>
466  </TargetQuantitationType_assnref>
467      </Error>
468      <Error name="rBGPixSDev" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGPixSDev" isBackground="true">
469  <Descriptions_assnlist>
470    <Description text="Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel."/>
471  </Descriptions_assnlist>
472  <Channel_assnref>
473    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
474  </Channel_assnref>
475  <Scale_assn>
476    <OntologyEntry value="linear_scale" category="Scale"/>
477  </Scale_assn>
478  <DataType_assn>
479    <OntologyEntry value="float" category="DataType"/>
480  </DataType_assn>
481  <TargetQuantitationType_assnref>
482    <MeasuredSignal_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGMeanSignal"/>
483  </TargetQuantitationType_assnref>
484      </Error>
485      <SpecializedQuantitationType name="gNumSatPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gNumSatPix" isBackground="false">
486  <Descriptions_assnlist>
487    <Description text="Total number of saturated pixels per feature, computed per channel."/>
488  </Descriptions_assnlist>
489  <Channel_assnref>
490    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
491  </Channel_assnref>
492  <Scale_assn>
493    <OntologyEntry value="linear_scale" category="Scale"/>
494  </Scale_assn>
495  <DataType_assn>
496    <OntologyEntry value="integer" category="DataType"/>
497  </DataType_assn>
498      </SpecializedQuantitationType>
499      <SpecializedQuantitationType name="rNumSatPix" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rNumSatPix" isBackground="false">
500  <Descriptions_assnlist>
501    <Description text="Total number of saturated pixels per feature, computed per channel."/>
502  </Descriptions_assnlist>
503  <Channel_assnref>
504    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
505  </Channel_assnref>
506  <Scale_assn>
507    <OntologyEntry value="linear_scale" category="Scale"/>
508  </Scale_assn>
509  <DataType_assn>
510    <OntologyEntry value="integer" category="DataType"/>
511  </DataType_assn>
512      </SpecializedQuantitationType>
513      <SpecializedQuantitationType name="gIsSaturated" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsSaturated" isBackground="false">
514  <Descriptions_assnlist>
515    <Description text="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."/>
516  </Descriptions_assnlist>
517  <Channel_assnref>
518    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
519  </Channel_assnref>
520  <Scale_assn>
521    <OntologyEntry value="linear_scale" category="Scale"/>
522  </Scale_assn>
523  <DataType_assn>
524    <OntologyEntry value="boolean" category="DataType"/>
525  </DataType_assn>
526      </SpecializedQuantitationType>
527      <SpecializedQuantitationType name="rIsSaturated" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsSaturated" isBackground="false">
528  <Descriptions_assnlist>
529    <Description text="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."/>
530  </Descriptions_assnlist>
531  <Channel_assnref>
532    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
533  </Channel_assnref>
534  <Scale_assn>
535    <OntologyEntry value="linear_scale" category="Scale"/>
536  </Scale_assn>
537  <DataType_assn>
538    <OntologyEntry value="boolean" category="DataType"/>
539  </DataType_assn>
540      </SpecializedQuantitationType>
541      <SpecializedQuantitationType name="PixCorrelation" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:PixCorrelation" isBackground="false">
542  <Descriptions_assnlist>
543    <Description text="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."/>
544  </Descriptions_assnlist>
545  <Scale_assn>
546    <OntologyEntry value="linear_scale" category="Scale"/>
547  </Scale_assn>
548  <DataType_assn>
549    <OntologyEntry value="float" category="DataType"/>
550  </DataType_assn>
551      </SpecializedQuantitationType>
552      <SpecializedQuantitationType name="BGPixCorrelation" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:BGPixCorrelation" isBackground="true">
553  <Descriptions_assnlist>
554    <Description text="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."/>
555  </Descriptions_assnlist>
556  <Scale_assn>
557    <OntologyEntry value="linear_scale" category="Scale"/>
558  </Scale_assn>
559  <DataType_assn>
560    <OntologyEntry value="float" category="DataType"/>
561  </DataType_assn>
562      </SpecializedQuantitationType>
563      <SpecializedQuantitationType name="gIsFeatNonUnifOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsFeatNonUnifOL" isBackground="false">
564  <Descriptions_assnlist>
565    <Description text="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."/>
566  </Descriptions_assnlist>
567  <Channel_assnref>
568    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
569  </Channel_assnref>
570  <Scale_assn>
571    <OntologyEntry value="linear_scale" category="Scale"/>
572  </Scale_assn>
573  <DataType_assn>
574    <OntologyEntry value="boolean" category="DataType"/>
575  </DataType_assn>
576      </SpecializedQuantitationType>
577      <SpecializedQuantitationType name="rIsFeatNonUnifOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsFeatNonUnifOL" isBackground="false">
578  <Descriptions_assnlist>
579    <Description text="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."/>
580  </Descriptions_assnlist>
581  <Channel_assnref>
582    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
583  </Channel_assnref>
584  <Scale_assn>
585    <OntologyEntry value="linear_scale" category="Scale"/>
586  </Scale_assn>
587  <DataType_assn>
588    <OntologyEntry value="boolean" category="DataType"/>
589  </DataType_assn>
590      </SpecializedQuantitationType>
591      <SpecializedQuantitationType name="gIsBGNonUnifOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsBGNonUnifOL" isBackground="true">
592  <Descriptions_assnlist>
593    <Description text="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."/>
594  </Descriptions_assnlist>
595  <Channel_assnref>
596    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
597  </Channel_assnref>
598  <Scale_assn>
599    <OntologyEntry value="linear_scale" category="Scale"/>
600  </Scale_assn>
601  <DataType_assn>
602    <OntologyEntry value="boolean" category="DataType"/>
603  </DataType_assn>
604      </SpecializedQuantitationType>
605      <SpecializedQuantitationType name="rIsBGNonUnifOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsBGNonUnifOL" isBackground="true">
606  <Descriptions_assnlist>
607    <Description text="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."/>
608  </Descriptions_assnlist>
609  <Channel_assnref>
610    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
611  </Channel_assnref>
612  <Scale_assn>
613    <OntologyEntry value="linear_scale" category="Scale"/>
614  </Scale_assn>
615  <DataType_assn>
616    <OntologyEntry value="boolean" category="DataType"/>
617  </DataType_assn>
618      </SpecializedQuantitationType>
619      <SpecializedQuantitationType name="gIsFeatPopnOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsFeatPopnOL" isBackground="false">
620  <Descriptions_assnlist>
621    <Description text="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."/>
622  </Descriptions_assnlist>
623  <Channel_assnref>
624    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
625  </Channel_assnref>
626  <Scale_assn>
627    <OntologyEntry value="linear_scale" category="Scale"/>
628  </Scale_assn>
629  <DataType_assn>
630    <OntologyEntry value="boolean" category="DataType"/>
631  </DataType_assn>
632      </SpecializedQuantitationType>
633      <SpecializedQuantitationType name="rIsFeatPopnOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsFeatPopnOL" isBackground="false">
634  <Descriptions_assnlist>
635    <Description text="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."/>
636  </Descriptions_assnlist>
637  <Channel_assnref>
638    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
639  </Channel_assnref>
640  <Scale_assn>
641    <OntologyEntry value="linear_scale" category="Scale"/>
642  </Scale_assn>
643  <DataType_assn>
644    <OntologyEntry value="boolean" category="DataType"/>
645  </DataType_assn>
646      </SpecializedQuantitationType>
647      <SpecializedQuantitationType name="gIsBGPopnOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsBGPopnOL" isBackground="true">
648  <Descriptions_assnlist>
649    <Description text="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."/>
650  </Descriptions_assnlist>
651  <Channel_assnref>
652    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
653  </Channel_assnref>
654  <Scale_assn>
655    <OntologyEntry value="linear_scale" category="Scale"/>
656  </Scale_assn>
657  <DataType_assn>
658    <OntologyEntry value="boolean" category="DataType"/>
659  </DataType_assn>
660      </SpecializedQuantitationType>
661      <SpecializedQuantitationType name="rIsBGPopnOL" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsBGPopnOL" isBackground="true">
662  <Descriptions_assnlist>
663    <Description text="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."/>
664  </Descriptions_assnlist>
665  <Channel_assnref>
666    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
667  </Channel_assnref>
668  <Scale_assn>
669    <OntologyEntry value="linear_scale" category="Scale"/>
670  </Scale_assn>
671  <DataType_assn>
672    <OntologyEntry value="boolean" category="DataType"/>
673  </DataType_assn>
674      </SpecializedQuantitationType>
675      <SpecializedQuantitationType name="IsManualFlag" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:IsManualFlag" isBackground="false">
676  <Descriptions_assnlist>
677    <Description text="If a feature has been moved manually this flag will be set to 1."/>
678  </Descriptions_assnlist>
679  <Scale_assn>
680    <OntologyEntry value="linear_scale" category="Scale"/>
681  </Scale_assn>
682  <DataType_assn>
683    <OntologyEntry value="boolean" category="DataType"/>
684  </DataType_assn>
685      </SpecializedQuantitationType>
686      <SpecializedQuantitationType name="gBGSubSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGSubSignal" isBackground="false">
687  <Descriptions_assnlist>
688    <Description text="The net green signal following the subtraction of the background from the raw mean green signal."/>
689  </Descriptions_assnlist>
690  <Channel_assnref>
691    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
692  </Channel_assnref>
693  <Scale_assn>
694    <OntologyEntry value="linear_scale" category="Scale"/>
695  </Scale_assn>
696  <DataType_assn>
697    <OntologyEntry value="float" category="DataType"/>
698  </DataType_assn>
699      </SpecializedQuantitationType>
700      <SpecializedQuantitationType name="rBGSubSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGSubSignal" isBackground="false">
701  <Descriptions_assnlist>
702    <Description text="The net red signal following the subtraction of the background from the raw mean red signal."/>
703  </Descriptions_assnlist>
704  <Channel_assnref>
705    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
706  </Channel_assnref>
707  <Scale_assn>
708    <OntologyEntry value="linear_scale" category="Scale"/>
709  </Scale_assn>
710  <DataType_assn>
711    <OntologyEntry value="float" category="DataType"/>
712  </DataType_assn>
713      </SpecializedQuantitationType>
714      <Error name="gBGSubSigError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGSubSigError" isBackground="false">
715  <Descriptions_assnlist>
716    <Description text="Propagated standard error as computed on net green background subtracted signal."/>
717  </Descriptions_assnlist>
718  <Channel_assnref>
719    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
720  </Channel_assnref>
721  <Scale_assn>
722    <OntologyEntry value="linear_scale" category="Scale"/>
723  </Scale_assn>
724  <DataType_assn>
725    <OntologyEntry value="float" category="DataType"/>
726  </DataType_assn>
727  <TargetQuantitationType_assnref>
728    <SpecializedQuantitationType_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGSubSignal"/>
729  </TargetQuantitationType_assnref>
730      </Error>
731      <Error name="rBGSubSigError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGSubSigError" isBackground="false">
732  <Descriptions_assnlist>
733    <Description text="Propagated standard error as computed on net red background subtracted signal."/>
734  </Descriptions_assnlist>
735  <Channel_assnref>
736    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
737  </Channel_assnref>
738  <Scale_assn>
739    <OntologyEntry value="linear_scale" category="Scale"/>
740  </Scale_assn>
741  <DataType_assn>
742    <OntologyEntry value="float" category="DataType"/>
743  </DataType_assn>
744  <TargetQuantitationType_assnref>
745    <SpecializedQuantitationType_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGSubSignal"/>
746  </TargetQuantitationType_assnref>
747      </Error>
748      <SpecializedQuantitationType name="BGSubSigCorrelation" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:BGSubSigCorrelation" isBackground="false">
749  <Descriptions_assnlist>
750    <Description text="Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space."/>
751  </Descriptions_assnlist>
752  <Scale_assn>
753    <OntologyEntry value="linear_scale" category="Scale"/>
754  </Scale_assn>
755  <DataType_assn>
756    <OntologyEntry value="float" category="DataType"/>
757  </DataType_assn>
758      </SpecializedQuantitationType>
759      <SpecializedQuantitationType name="gIsPosAndSignif" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsPosAndSignif" isBackground="false">
760  <Descriptions_assnlist>
761    <Description text="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."/>
762  </Descriptions_assnlist>
763  <Channel_assnref>
764    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
765  </Channel_assnref>
766  <Scale_assn>
767    <OntologyEntry value="linear_scale" category="Scale"/>
768  </Scale_assn>
769  <DataType_assn>
770    <OntologyEntry value="boolean" category="DataType"/>
771  </DataType_assn>
772      </SpecializedQuantitationType>
773      <SpecializedQuantitationType name="rIsPosAndSignif" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsPosAndSignif" isBackground="false">
774  <Descriptions_assnlist>
775    <Description text="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."/>
776  </Descriptions_assnlist>
777  <Channel_assnref>
778    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
779  </Channel_assnref>
780  <Scale_assn>
781    <OntologyEntry value="linear_scale" category="Scale"/>
782  </Scale_assn>
783  <DataType_assn>
784    <OntologyEntry value="boolean" category="DataType"/>
785  </DataType_assn>
786      </SpecializedQuantitationType>
787      <SpecializedQuantitationType name="gPValFeatEqBG" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gPValFeatEqBG" isBackground="false">
788  <Descriptions_assnlist>
789    <Description text="P-value from t-test of significance between green Mean signal and green background."/>
790  </Descriptions_assnlist>
791  <Channel_assnref>
792    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
793  </Channel_assnref>
794  <Scale_assn>
795    <OntologyEntry value="linear_scale" category="Scale"/>
796  </Scale_assn>
797  <DataType_assn>
798    <OntologyEntry value="float" category="DataType"/>
799  </DataType_assn>
800      </SpecializedQuantitationType>
801      <SpecializedQuantitationType name="rPValFeatEqBG" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rPValFeatEqBG" isBackground="false">
802  <Descriptions_assnlist>
803    <Description text="P-value from t-test of significance between red Mean signal and red background."/>
804  </Descriptions_assnlist>
805  <Channel_assnref>
806    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
807  </Channel_assnref>
808  <Scale_assn>
809    <OntologyEntry value="linear_scale" category="Scale"/>
810  </Scale_assn>
811  <DataType_assn>
812    <OntologyEntry value="float" category="DataType"/>
813  </DataType_assn>
814      </SpecializedQuantitationType>
815      <SpecializedQuantitationType name="gNumBGUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gNumBGUsed" isBackground="false">
816  <Descriptions_assnlist>
817    <Description text="A count of the number of background pixels used in the green channel."/>
818  </Descriptions_assnlist>
819  <Channel_assnref>
820    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
821  </Channel_assnref>
822  <Scale_assn>
823    <OntologyEntry value="linear_scale" category="Scale"/>
824  </Scale_assn>
825  <DataType_assn>
826    <OntologyEntry value="integer" category="DataType"/>
827  </DataType_assn>
828      </SpecializedQuantitationType>
829      <SpecializedQuantitationType name="rNumBGUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rNumBGUsed" isBackground="false">
830  <Descriptions_assnlist>
831    <Description text="A count of the number of background pixels used in the red channel."/>
832  </Descriptions_assnlist>
833  <Channel_assnref>
834    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
835  </Channel_assnref>
836  <Scale_assn>
837    <OntologyEntry value="linear_scale" category="Scale"/>
838  </Scale_assn>
839  <DataType_assn>
840    <OntologyEntry value="integer" category="DataType"/>
841  </DataType_assn>
842      </SpecializedQuantitationType>
843      <SpecializedQuantitationType name="gIsWellAboveBG" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gIsWellAboveBG" isBackground="false">
844  <Descriptions_assnlist>
845    <Description text="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."/>
846  </Descriptions_assnlist>
847  <Channel_assnref>
848    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
849  </Channel_assnref>
850  <Scale_assn>
851    <OntologyEntry value="linear_scale" category="Scale"/>
852  </Scale_assn>
853  <DataType_assn>
854    <OntologyEntry value="boolean" category="DataType"/>
855  </DataType_assn>
856      </SpecializedQuantitationType>
857      <SpecializedQuantitationType name="rIsWellAboveBG" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rIsWellAboveBG" isBackground="false">
858  <Descriptions_assnlist>
859    <Description text="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."/>
860  </Descriptions_assnlist>
861  <Channel_assnref>
862    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
863  </Channel_assnref>
864  <Scale_assn>
865    <OntologyEntry value="linear_scale" category="Scale"/>
866  </Scale_assn>
867  <DataType_assn>
868    <OntologyEntry value="boolean" category="DataType"/>
869  </DataType_assn>
870      </SpecializedQuantitationType>
871      <SpecializedQuantitationType name="gBGUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGUsed" isBackground="false">
872  <Descriptions_assnlist>
873    <Description text="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."/>
874  </Descriptions_assnlist>
875  <Channel_assnref>
876    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
877  </Channel_assnref>
878  <Scale_assn>
879    <OntologyEntry value="linear_scale" category="Scale"/>
880  </Scale_assn>
881  <DataType_assn>
882    <OntologyEntry value="float" category="DataType"/>
883  </DataType_assn>
884      </SpecializedQuantitationType>
885      <SpecializedQuantitationType name="rBGUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGUsed" isBackground="false">
886  <Descriptions_assnlist>
887    <Description text="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."/>
888  </Descriptions_assnlist>
889  <Channel_assnref>
890    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
891  </Channel_assnref>
892  <Scale_assn>
893    <OntologyEntry value="linear_scale" category="Scale"/>
894  </Scale_assn>
895  <DataType_assn>
896    <OntologyEntry value="float" category="DataType"/>
897  </DataType_assn>
898      </SpecializedQuantitationType>
899      <Error name="gBGSDUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGSDUsed" isBackground="false">
900  <Descriptions_assnlist>
901    <Description text="Standard deviation of background used in green channel."/>
902  </Descriptions_assnlist>
903  <Channel_assnref>
904    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
905  </Channel_assnref>
906  <Scale_assn>
907    <OntologyEntry value="linear_scale" category="Scale"/>
908  </Scale_assn>
909  <DataType_assn>
910    <OntologyEntry value="float" category="DataType"/>
911  </DataType_assn>
912  <TargetQuantitationType_assnref>
913    <SpecializedQuantitationType_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gBGUsed"/>
914  </TargetQuantitationType_assnref>
915      </Error>
916      <Error name="rBGSDUsed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGSDUsed" isBackground="false">
917  <Descriptions_assnlist>
918    <Description text="Standard deviation of background used in red channel."/>
919  </Descriptions_assnlist>
920  <Channel_assnref>
921    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
922  </Channel_assnref>
923  <Scale_assn>
924    <OntologyEntry value="linear_scale" category="Scale"/>
925  </Scale_assn>
926  <DataType_assn>
927    <OntologyEntry value="float" category="DataType"/>
928  </DataType_assn>
929  <TargetQuantitationType_assnref>
930    <SpecializedQuantitationType_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rBGUsed"/>
931  </TargetQuantitationType_assnref>
932      </Error>
933      <SpecializedQuantitationType name="IsNormalization" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:IsNormalization" isBackground="false">
934  <Descriptions_assnlist>
935    <Description text="A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used."/>
936  </Descriptions_assnlist>
937  <Scale_assn>
938    <OntologyEntry value="linear_scale" category="Scale"/>
939  </Scale_assn>
940  <DataType_assn>
941    <OntologyEntry value="boolean" category="DataType"/>
942  </DataType_assn>
943      </SpecializedQuantitationType>
944      <SpecializedQuantitationType name="gDyeNormSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gDyeNormSignal" isBackground="false">
945  <Descriptions_assnlist>
946    <Description text="The dye normalized signal in the indicated channel."/>
947  </Descriptions_assnlist>
948  <Channel_assnref>
949    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
950  </Channel_assnref>
951  <Scale_assn>
952    <OntologyEntry value="linear_scale" category="Scale"/>
953  </Scale_assn>
954  <DataType_assn>
955    <OntologyEntry value="float" category="DataType"/>
956  </DataType_assn>
957      </SpecializedQuantitationType>
958      <SpecializedQuantitationType name="rDyeNormSignal" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rDyeNormSignal" isBackground="false">
959  <Descriptions_assnlist>
960    <Description text="The dye normalized signal in the indicated channel."/>
961  </Descriptions_assnlist>
962  <Channel_assnref>
963    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
964  </Channel_assnref>
965  <Scale_assn>
966    <OntologyEntry value="linear_scale" category="Scale"/>
967  </Scale_assn>
968  <DataType_assn>
969    <OntologyEntry value="float" category="DataType"/>
970  </DataType_assn>
971      </SpecializedQuantitationType>
972      <Error name="gDyeNormError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gDyeNormError" isBackground="false">
973  <Descriptions_assnlist>
974    <Description text="The standard error associated with the dye normalized signal."/>
975  </Descriptions_assnlist>
976  <Channel_assnref>
977    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
978  </Channel_assnref>
979  <Scale_assn>
980    <OntologyEntry value="linear_scale" category="Scale"/>
981  </Scale_assn>
982  <DataType_assn>
983    <OntologyEntry value="float" category="DataType"/>
984  </DataType_assn>
985  <TargetQuantitationType_assnref>
986    <SpecializedQuantitationType_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gDyeNormSignal"/>
987  </TargetQuantitationType_assnref>
988      </Error>
989      <Error name="rDyeNormError" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rDyeNormError" isBackground="false">
990  <Descriptions_assnlist>
991    <Description text="The standard error associated with the dye normalized signal."/>
992  </Descriptions_assnlist>
993  <Channel_assnref>
994    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
995  </Channel_assnref>
996  <Scale_assn>
997    <OntologyEntry value="linear_scale" category="Scale"/>
998  </Scale_assn>
999  <DataType_assn>
1000    <OntologyEntry value="float" category="DataType"/>
1001  </DataType_assn>
1002  <TargetQuantitationType_assnref>
1003    <Error_ref identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rDyeNormSignal"/>
1004  </TargetQuantitationType_assnref>
1005      </Error>
1006      <SpecializedQuantitationType name="DyeNormCorrelation" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:DyeNormCorrelation" isBackground="false">
1007  <Descriptions_assnlist>
1008    <Description text="Dye normalized red and green pixel correlation."/>
1009  </Descriptions_assnlist>
1010  <Scale_assn>
1011    <OntologyEntry value="linear_scale" category="Scale"/>
1012  </Scale_assn>
1013  <DataType_assn>
1014    <OntologyEntry value="float" category="DataType"/>
1015  </DataType_assn>
1016      </SpecializedQuantitationType>
1017      <SpecializedQuantitationType name="ErrorModel" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:ErrorModel" isBackground="false">
1018  <Descriptions_assnlist>
1019    <Description text="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."/>
1020  </Descriptions_assnlist>
1021  <Scale_assn>
1022    <OntologyEntry value="linear_scale" category="Scale"/>
1023  </Scale_assn>
1024  <DataType_assn>
1025    <OntologyEntry value="integer" category="DataType"/>
1026  </DataType_assn>
1027      </SpecializedQuantitationType>
1028      <SpecializedQuantitationType name="xDev" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:xDev" isBackground="false">
1029  <Descriptions_assnlist>
1030    <Description text="Used to compute the Log Ratio PValue."/>
1031  </Descriptions_assnlist>
1032  <Scale_assn>
1033    <OntologyEntry value="log_base_10" category="Scale"/>
1034  </Scale_assn>
1035  <DataType_assn>
1036    <OntologyEntry value="float" category="DataType"/>
1037  </DataType_assn>
1038      </SpecializedQuantitationType>
1039      <SpecializedQuantitationType name="gSpatialDetrendIsInFilteredSet" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gSpatialDetrendIsInFilteredSet" isBackground="false">
1040  <Descriptions_assnlist>
1041    <Description text="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."/>
1042  </Descriptions_assnlist>
1043  <Channel_assnref>
1044    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
1045  </Channel_assnref>
1046  <Scale_assn>
1047    <OntologyEntry value="linear_scale" category="Scale"/>
1048  </Scale_assn>
1049  <DataType_assn>
1050    <OntologyEntry value="boolean" category="DataType"/>
1051  </DataType_assn>
1052      </SpecializedQuantitationType>
1053      <SpecializedQuantitationType name="rSpatialDetrendIsInFilteredSet" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rSpatialDetrendIsInFilteredSet" isBackground="false">
1054  <Descriptions_assnlist>
1055    <Description text="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."/>
1056  </Descriptions_assnlist>
1057  <Channel_assnref>
1058    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1059  </Channel_assnref>
1060  <Scale_assn>
1061    <OntologyEntry value="linear_scale" category="Scale"/>
1062  </Scale_assn>
1063  <DataType_assn>
1064    <OntologyEntry value="boolean" category="DataType"/>
1065  </DataType_assn>
1066      </SpecializedQuantitationType>
1067      <SpecializedQuantitationType name="gSpatialDetrendSurfaceValue" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:gSpatialDetrendSurfaceValue" isBackground="false">
1068  <Descriptions_assnlist>
1069    <Description text="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."/>
1070  </Descriptions_assnlist>
1071  <Channel_assnref>
1072    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
1073  </Channel_assnref>
1074  <Scale_assn>
1075    <OntologyEntry value="linear_scale" category="Scale"/>
1076  </Scale_assn>
1077  <DataType_assn>
1078    <OntologyEntry value="float" category="DataType"/>
1079  </DataType_assn>
1080      </SpecializedQuantitationType>
1081      <SpecializedQuantitationType name="rSpatialDetrendSurfaceValue" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:rSpatialDetrendSurfaceValue" isBackground="false">
1082  <Descriptions_assnlist>
1083    <Description text="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."/>
1084  </Descriptions_assnlist>
1085  <Channel_assnref>
1086    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1087  </Channel_assnref>
1088  <Scale_assn>
1089    <OntologyEntry value="linear_scale" category="Scale"/>
1090  </Scale_assn>
1091  <DataType_assn>
1092    <OntologyEntry value="float" category="DataType"/>
1093  </DataType_assn>
1094      </SpecializedQuantitationType>
1095      <Failed name="Failed" identifier="Agilent Technologies:Feature Extraction Software_QuantitationType:Failed" isBackground="false">
1096  <Descriptions_assnlist>
1097    <Description text="Set to one if the quantitation values of a feature are considered bad enough to thrown out in the higher level analysis. Features are thrown out if both channels are saturated or if either channel is a non-uniform outlier. A feature can be failed from outside of feature extraction via setting this flag when loading the design or grid."/>
1098  </Descriptions_assnlist>
1099  <Scale_assn>
1100    <OntologyEntry value="linear_scale" category="Scale"/>
1101  </Scale_assn>
1102  <DataType_assn>
1103    <OntologyEntry value="boolean" category="DataType"/>
1104  </DataType_assn>
1105      </Failed>
1106    </QuantitationType_assnlist>
1107  </QuantitationType_package>
1108</MAGE-ML>
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