source: trunk/misc/mage/rawdatatypes/QT_ChipSkipper.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: 27.4 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
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="EBI:eleh:ChipSkipper QT XML">
5  <QuantitationType_package>
6    <QuantitationType_assnlist>
7      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Line_Counter" name="Line_Counter" isBackground="0">
8  <Descriptions_assnlist>
9    <Description text="Line counter">
10    </Description>
11  </Descriptions_assnlist>
12  <Scale_assn>
13    <OntologyEntry category="Scale" value="unscaled">
14    </OntologyEntry>
15  </Scale_assn>
16  <DataType_assn>
17    <OntologyEntry category="DataType" value="integer">
18    </OntologyEntry>
19  </DataType_assn>
20      </SpecializedQuantitationType>
21
22      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Flags" name="Flags" isBackground="0">
23  <Descriptions_assnlist>
24    <Description text="Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad.">
25    </Description>
26  </Descriptions_assnlist>
27  <Scale_assn>
28    <OntologyEntry category="Scale" value="unscaled">
29    </OntologyEntry>
30  </Scale_assn>
31  <DataType_assn>
32    <OntologyEntry category="DataType" value="string_datatype">
33    </OntologyEntry>
34  </DataType_assn>
35      </SpecializedQuantitationType>
36
37      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:GS_Flags" name="GS_Flags" isBackground="0">
38  <Descriptions_assnlist>
39    <Description text="P = pass or M = marginal flag.">
40    </Description>
41  </Descriptions_assnlist>
42  <Scale_assn>
43    <OntologyEntry category="Scale" value="linear_scale">
44    </OntologyEntry>
45  </Scale_assn>
46  <DataType_assn>
47    <OntologyEntry category="DataType" value="string_datatype">
48    </OntologyEntry>
49  </DataType_assn>
50      </SpecializedQuantitationType>
51
52      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Image-x-Pos" name="Image-x-Pos" isBackground="0">
53  <Descriptions_assnlist>
54    <Description text="Image coordinate of spot.">
55    </Description>
56  </Descriptions_assnlist>
57  <Scale_assn>
58    <OntologyEntry category="Scale" value="linear_scale">
59    </OntologyEntry>
60  </Scale_assn>
61  <DataType_assn>
62    <OntologyEntry category="DataType" value="integer">
63    </OntologyEntry>
64  </DataType_assn>
65      </SpecializedQuantitationType>
66
67      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Image-y-Pos" name="Image-y-Pos" isBackground="0">
68  <Descriptions_assnlist>
69    <Description text="Image coordinate of spot.">
70    </Description>
71  </Descriptions_assnlist>
72  <Scale_assn>
73    <OntologyEntry category="Scale" value="linear_scale">
74    </OntologyEntry>
75  </Scale_assn>
76  <DataType_assn>
77    <OntologyEntry category="DataType" value="integer">
78    </OntologyEntry>
79  </DataType_assn>
80      </SpecializedQuantitationType>
81
82      <MeasuredSignal identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Volume" name="Cy3_Volume" isBackground="0">
83  <Descriptions_assnlist>
84    <Description text="Total integrated signal intensity in color channel Cy3.">
85    </Description>
86  </Descriptions_assnlist>
87  <Channel_assnref>
88    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
89  </Channel_assnref>
90  <Scale_assn>
91    <OntologyEntry category="Scale" value="linear_scale">
92    </OntologyEntry>
93  </Scale_assn>
94  <DataType_assn>
95    <OntologyEntry category="DataType" value="integer">
96    </OntologyEntry>
97  </DataType_assn>
98      </MeasuredSignal>
99
100      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Av-Vol/pixel" name="Cy3_Av-Vol/pixel" isBackground="0">
101  <Descriptions_assnlist>
102    <Description text="Average intensity per pixel in color channel Cy3.">
103    </Description>
104  </Descriptions_assnlist>
105  <Channel_assnref>
106    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
107  </Channel_assnref>
108  <Scale_assn>
109    <OntologyEntry category="Scale" value="linear_scale">
110    </OntologyEntry>
111  </Scale_assn>
112  <DataType_assn>
113    <OntologyEntry category="DataType" value="float">
114    </OntologyEntry>
115  </DataType_assn>
116      </SpecializedQuantitationType>
117
118      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_BG-Arith" name="Cy3_BG-Arith" isBackground="1">
119  <Descriptions_assnlist>
120    <Description text="Arithmetic average for local background in color channel Cy3.">
121    </Description>
122  </Descriptions_assnlist>
123  <Channel_assnref>
124    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
125  </Channel_assnref>
126  <Scale_assn>
127    <OntologyEntry category="Scale" value="linear_scale">
128    </OntologyEntry>
129  </Scale_assn>
130  <DataType_assn>
131    <OntologyEntry category="DataType" value="float">
132    </OntologyEntry>
133  </DataType_assn>
134      </SpecializedQuantitationType>
135
136      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_BG-Geom" name="Cy3_BG-Geom" isBackground="1">
137  <Descriptions_assnlist>
138    <Description text="Geometric average for local background in color channel Cy3.">
139    </Description>
140  </Descriptions_assnlist>
141  <Channel_assnref>
142    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
143  </Channel_assnref>
144  <Scale_assn>
145    <OntologyEntry category="Scale" value="linear_scale">
146    </OntologyEntry>
147  </Scale_assn>
148  <DataType_assn>
149    <OntologyEntry category="DataType" value="float">
150    </OntologyEntry>
151  </DataType_assn>
152      </SpecializedQuantitationType>
153
154      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_BG-Median" name="Cy3_BG-Median" isBackground="1">
155  <Descriptions_assnlist>
156    <Description text="Median average for local background in color channel Cy3.">
157    </Description>
158  </Descriptions_assnlist>
159  <Channel_assnref>
160    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
161  </Channel_assnref>
162  <Scale_assn>
163    <OntologyEntry category="Scale" value="linear_scale">
164    </OntologyEntry>
165  </Scale_assn>
166  <DataType_assn>
167    <OntologyEntry category="DataType" value="float">
168    </OntologyEntry>
169  </DataType_assn>
170      </SpecializedQuantitationType>
171
172      <MeasuredSignal identifier="EMBL:ChipSkipper_QuantitationType:Cy3_BG_Tot" name="Cy3_BG_Tot" isBackground="1">
173  <Descriptions_assnlist>
174    <Description text="Total integrated background in color channel Cy3.">
175    </Description>
176  </Descriptions_assnlist>
177  <Channel_assnref>
178    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
179  </Channel_assnref>
180  <Scale_assn>
181    <OntologyEntry category="Scale" value="linear_scale">
182    </OntologyEntry>
183  </Scale_assn>
184  <DataType_assn>
185    <OntologyEntry category="DataType" value="float">
186    </OntologyEntry>
187  </DataType_assn>
188      </MeasuredSignal>
189
190      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Vol-BG" name="Cy3_Vol-BG" isBackground="0">
191  <Descriptions_assnlist>
192    <Description text="Background reduced intensity of colour channel Cy3.">
193    </Description>
194  </Descriptions_assnlist>
195  <Channel_assnref>
196    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
197  </Channel_assnref>
198  <Scale_assn>
199    <OntologyEntry category="Scale" value="linear_scale">
200    </OntologyEntry>
201  </Scale_assn>
202  <DataType_assn>
203    <OntologyEntry category="DataType" value="float">
204    </OntologyEntry>
205  </DataType_assn>
206      </SpecializedQuantitationType>
207
208      <Error identifier="EMBL:ChipSkipper_QuantitationType:Cy3_SNR1" name="Cy3_SNR1" isBackground="1">
209  <Descriptions_assnlist>
210    <Description text="Sdev of local background average in color channel Cy3.">
211    </Description>
212  </Descriptions_assnlist>
213  <Channel_assnref>
214    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
215  </Channel_assnref>
216  <Scale_assn>
217    <OntologyEntry category="Scale" value="linear_scale">
218    </OntologyEntry>
219  </Scale_assn>
220  <DataType_assn>
221    <OntologyEntry category="DataType" value="float">
222    </OntologyEntry>
223  </DataType_assn>
224  <TargetQuantitationType_assnref>
225    <SpecializedQuantitationType_ref identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Vol-BG"/>
226  </TargetQuantitationType_assnref>
227      </Error>
228
229      <Error identifier="EMBL:ChipSkipper_QuantitationType:Cy3_SNR1_Score" name="Cy3_SNR1_Score" isBackground="1">
230  <Descriptions_assnlist>
231    <Description text="Quality value based on intensity and background for color channel Cy3 (range: 0 = bad....1 = good).">
232    </Description>
233  </Descriptions_assnlist>
234  <Channel_assnref>
235    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
236  </Channel_assnref>
237  <Scale_assn>
238    <OntologyEntry category="Scale" value="linear_scale">
239    </OntologyEntry>
240  </Scale_assn>
241  <DataType_assn>
242    <OntologyEntry category="DataType" value="float">
243    </OntologyEntry>
244  </DataType_assn>
245  <TargetQuantitationType_assnref>
246    <SpecializedQuantitationType_ref identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Vol-BG"/>
247  </TargetQuantitationType_assnref>
248      </Error>
249
250      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Spot-area" name="Cy3_Spot-area" isBackground="0">
251  <Descriptions_assnlist>
252    <Description text="Area of spot in colour channel Cy3 in pixels.">
253    </Description>
254  </Descriptions_assnlist>
255  <Channel_assnref>
256    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
257  </Channel_assnref>
258  <Scale_assn>
259    <OntologyEntry category="Scale" value="linear_scale">
260    </OntologyEntry>
261  </Scale_assn>
262  <DataType_assn>
263    <OntologyEntry category="DataType" value="float">
264    </OntologyEntry>
265  </DataType_assn>
266      </SpecializedQuantitationType>
267
268      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy3_Sat-pixel" name="Cy3_Sat-pixel" isBackground="0">
269  <Descriptions_assnlist>
270    <Description text="Number of saturated pixel in color channel Cy3.">
271    </Description>
272  </Descriptions_assnlist>
273  <Channel_assnref>
274    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
275  </Channel_assnref>
276  <Scale_assn>
277    <OntologyEntry category="Scale" value="linear_scale">
278    </OntologyEntry>
279  </Scale_assn>
280  <DataType_assn>
281    <OntologyEntry category="DataType" value="float">
282    </OntologyEntry>
283  </DataType_assn>
284      </SpecializedQuantitationType>
285
286      <MeasuredSignal identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Volume" name="Cy5_Volume" isBackground="0">
287  <Descriptions_assnlist>
288    <Description text="Total integrated signal intensity in color channel Cy5.">
289    </Description>
290  </Descriptions_assnlist>
291  <Channel_assnref>
292    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
293  </Channel_assnref>
294  <Scale_assn>
295    <OntologyEntry category="Scale" value="linear_scale">
296    </OntologyEntry>
297  </Scale_assn>
298  <DataType_assn>
299    <OntologyEntry category="DataType" value="integer">
300    </OntologyEntry>
301  </DataType_assn>
302      </MeasuredSignal>
303
304      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Av-Vol/pixel" name="Cy5_Av-Vol/pixel" isBackground="0">
305  <Descriptions_assnlist>
306    <Description text="Average intensity per pixel in color channel Cy5.">
307    </Description>
308  </Descriptions_assnlist>
309  <Channel_assnref>
310    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
311  </Channel_assnref>
312  <Scale_assn>
313    <OntologyEntry category="Scale" value="linear_scale">
314    </OntologyEntry>
315  </Scale_assn>
316  <DataType_assn>
317    <OntologyEntry category="DataType" value="float">
318    </OntologyEntry>
319  </DataType_assn>
320      </SpecializedQuantitationType>
321
322      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_BG-Arith" name="Cy5_BG-Arith" isBackground="1">
323  <Descriptions_assnlist>
324    <Description text="Arithmetic average for local background in color channel Cy5.">
325    </Description>
326  </Descriptions_assnlist>
327  <Channel_assnref>
328    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
329  </Channel_assnref>
330  <Scale_assn>
331    <OntologyEntry category="Scale" value="linear_scale">
332    </OntologyEntry>
333  </Scale_assn>
334  <DataType_assn>
335    <OntologyEntry category="DataType" value="float">
336    </OntologyEntry>
337  </DataType_assn>
338      </SpecializedQuantitationType>
339
340      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_BG-Geom" name="Cy5_BG-Geom" isBackground="1">
341  <Descriptions_assnlist>
342    <Description text="Geometric average for local background in color channel Cy5.">
343    </Description>
344  </Descriptions_assnlist>
345  <Channel_assnref>
346    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
347  </Channel_assnref>
348  <Scale_assn>
349    <OntologyEntry category="Scale" value="linear_scale">
350    </OntologyEntry>
351  </Scale_assn>
352  <DataType_assn>
353    <OntologyEntry category="DataType" value="float">
354    </OntologyEntry>
355  </DataType_assn>
356      </SpecializedQuantitationType>
357
358      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_BG-Median" name="Cy5_BG-Median" isBackground="1">
359  <Descriptions_assnlist>
360    <Description text="Median average for local background in color channel Cy5.">
361    </Description>
362  </Descriptions_assnlist>
363  <Channel_assnref>
364    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
365  </Channel_assnref>
366  <Scale_assn>
367    <OntologyEntry category="Scale" value="linear_scale">
368    </OntologyEntry>
369  </Scale_assn>
370  <DataType_assn>
371    <OntologyEntry category="DataType" value="float">
372    </OntologyEntry>
373  </DataType_assn>
374      </SpecializedQuantitationType>
375
376      <MeasuredSignal identifier="EMBL:ChipSkipper_QuantitationType:Cy5_BG_Tot" name="Cy5_BG_Tot" isBackground="1">
377  <Descriptions_assnlist>
378    <Description text="Total integrated background in color channel Cy5.">
379    </Description>
380  </Descriptions_assnlist>
381  <Channel_assnref>
382    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
383  </Channel_assnref>
384  <Scale_assn>
385    <OntologyEntry category="Scale" value="linear_scale">
386    </OntologyEntry>
387  </Scale_assn>
388  <DataType_assn>
389    <OntologyEntry category="DataType" value="float">
390    </OntologyEntry>
391  </DataType_assn>
392      </MeasuredSignal>
393
394      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Vol-BG" name="Cy5_Vol-BG" isBackground="0">
395  <Descriptions_assnlist>
396    <Description text="Background reduced intensity of colour channel Cy5.">
397    </Description>
398  </Descriptions_assnlist>
399  <Channel_assnref>
400    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
401  </Channel_assnref>
402  <Scale_assn>
403    <OntologyEntry category="Scale" value="linear_scale">
404    </OntologyEntry>
405  </Scale_assn>
406  <DataType_assn>
407    <OntologyEntry category="DataType" value="float">
408    </OntologyEntry>
409  </DataType_assn>
410      </SpecializedQuantitationType>
411
412      <Error identifier="EMBL:ChipSkipper_QuantitationType:Cy5_SNR1" name="Cy5_SNR1" isBackground="1">
413  <Descriptions_assnlist>
414    <Description text="Sdev of local background average in color channel Cy5.">
415    </Description>
416  </Descriptions_assnlist>
417  <Channel_assnref>
418    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
419  </Channel_assnref>
420  <Scale_assn>
421    <OntologyEntry category="Scale" value="linear_scale">
422    </OntologyEntry>
423  </Scale_assn>
424  <DataType_assn>
425    <OntologyEntry category="DataType" value="float">
426    </OntologyEntry>
427  </DataType_assn>
428  <TargetQuantitationType_assnref>
429    <SpecializedQuantitationType_ref identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Vol-BG"/>
430  </TargetQuantitationType_assnref>
431      </Error>
432
433      <Error identifier="EMBL:ChipSkipper_QuantitationType:Cy5_SNR1_Score" name="Cy5_SNR1_Score" isBackground="1">
434  <Descriptions_assnlist>
435    <Description text="Quality value based on intensity and background for color channel Cy5 (range: 0 = bad....1 = good).">
436    </Description>
437  </Descriptions_assnlist>
438  <Channel_assnref>
439    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
440  </Channel_assnref>
441  <Scale_assn>
442    <OntologyEntry category="Scale" value="linear_scale">
443    </OntologyEntry>
444  </Scale_assn>
445  <DataType_assn>
446    <OntologyEntry category="DataType" value="float">
447    </OntologyEntry>
448  </DataType_assn>
449  <TargetQuantitationType_assnref>
450    <SpecializedQuantitationType_ref identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Vol-BG"/>
451  </TargetQuantitationType_assnref>
452      </Error>
453
454      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Spot-area" name="Cy5_Spot-area" isBackground="0">
455  <Descriptions_assnlist>
456    <Description text="Area of spot in colour channel Cy5 in pixels.">
457    </Description>
458  </Descriptions_assnlist>
459  <Channel_assnref>
460    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
461  </Channel_assnref>
462  <Scale_assn>
463    <OntologyEntry category="Scale" value="linear_scale">
464    </OntologyEntry>
465  </Scale_assn>
466  <DataType_assn>
467    <OntologyEntry category="DataType" value="float">
468    </OntologyEntry>
469  </DataType_assn>
470      </SpecializedQuantitationType>
471
472      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Cy5_Sat-pixel" name="Cy5_Sat-pixel" isBackground="0">
473  <Descriptions_assnlist>
474    <Description text="Number of saturated pixel in color channel Cy5.">
475    </Description>
476  </Descriptions_assnlist>
477  <Channel_assnref>
478    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
479  </Channel_assnref>
480  <Scale_assn>
481    <OntologyEntry category="Scale" value="linear_scale">
482    </OntologyEntry>
483  </Scale_assn>
484  <DataType_assn>
485    <OntologyEntry category="DataType" value="float">
486    </OntologyEntry>
487  </DataType_assn>
488      </SpecializedQuantitationType>
489
490      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Rep_vol_BG2" name="Rep_vol_BG2" isBackground="0">
491  <Descriptions_assnlist>
492    <Description text="Average of background reduced volume for onchip replicas (when calculated).">
493    </Description>
494  </Descriptions_assnlist>
495  <Scale_assn>
496    <OntologyEntry category="Scale" value="linear_scale">
497    </OntologyEntry>
498  </Scale_assn>
499  <DataType_assn>
500    <OntologyEntry category="DataType" value="float">
501    </OntologyEntry>
502  </DataType_assn>
503      </SpecializedQuantitationType>
504
505      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Ratio-Cy5/Cy3" name="Ratio-Cy5/Cy3" isBackground="0">
506  <Descriptions_assnlist>
507    <Description text="Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )">
508    </Description>
509  </Descriptions_assnlist>
510  <Scale_assn>
511    <OntologyEntry category="Scale" value="linear_scale">
512    </OntologyEntry>
513  </Scale_assn>
514  <DataType_assn>
515    <OntologyEntry category="DataType" value="float">
516    </OntologyEntry>
517  </DataType_assn>
518      </SpecializedQuantitationType>
519
520      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Directional_Ratio-Cy5/Cy3" name="Directional_Ratio-Cy5/Cy3" isBackground="0">
521  <Descriptions_assnlist>
522    <Description text="Directional ratio: if Ratio &gt; 1 then Directional = Ratio, if Ratio &lt; 1 then Directional = -1/Ratio.">
523    </Description>
524  </Descriptions_assnlist>
525
526  <Scale_assn>
527    <OntologyEntry category="Scale" value="linear_scale">
528    </OntologyEntry>
529  </Scale_assn>
530  <DataType_assn>
531    <OntologyEntry category="DataType" value="float">
532    </OntologyEntry>
533  </DataType_assn>
534      </SpecializedQuantitationType>
535
536      <Ratio identifier="EMBL:ChipSkipper_QuantitationType:Log2_Ratio-Cy5/Cy3" name="Log2_Ratio-Cy5/Cy3" isBackground="0">
537  <Descriptions_assnlist>
538    <Description text="Log2 ratio: log2 (Ratio-Cy5/Cy3)">
539    </Description>
540  </Descriptions_assnlist>
541  <Scale_assn>
542    <OntologyEntry category="Scale" value="log_base_2">
543    </OntologyEntry>
544  </Scale_assn>
545  <DataType_assn>
546    <OntologyEntry category="DataType" value="float">
547    </OntologyEntry>
548  </DataType_assn>
549      </Ratio>
550
551      <DerivedSignal identifier="EMBL:ChipSkipper_QuantitationType:Comp_Channel Cy5" name="Comp_Channel Cy5" isBackground="0">
552  <Descriptions_assnlist>
553    <Description text="Normalised intensity of Cy5_Vol-BG.">
554    </Description>
555  </Descriptions_assnlist>
556  <Channel_assnref>
557    <Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
558  </Channel_assnref>
559  <Scale_assn>
560    <OntologyEntry category="Scale" value="linear_scale">
561    </OntologyEntry>
562  </Scale_assn>
563  <DataType_assn>
564    <OntologyEntry category="DataType" value="float">
565    </OntologyEntry>
566  </DataType_assn>
567      </DerivedSignal>
568
569      <DerivedSignal identifier="EMBL:ChipSkipper_QuantitationType:Comp_Channel Cy3" name="Comp_Channel Cy3" isBackground="0">
570  <Descriptions_assnlist>
571    <Description text="Normalised intensity of Cy3_Vol-BG.">
572    </Description>
573  </Descriptions_assnlist>
574  <Channel_assnref>
575    <Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
576  </Channel_assnref>
577  <Scale_assn>
578    <OntologyEntry category="Scale" value="linear_scale">
579    </OntologyEntry>
580  </Scale_assn>
581  <DataType_assn>
582    <OntologyEntry category="DataType" value="float">
583    </OntologyEntry>
584  </DataType_assn>
585      </DerivedSignal>
586
587      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Comp_Ratio-Cy5/Cy3" name="Comp_Ratio-Cy5/Cy3" isBackground="0">
588  <Descriptions_assnlist>
589    <Description text="Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 ).">
590    </Description>
591  </Descriptions_assnlist>
592  <Scale_assn>
593    <OntologyEntry category="Scale" value="linear_scale">
594    </OntologyEntry>
595  </Scale_assn>
596  <DataType_assn>
597    <OntologyEntry category="DataType" value="float">
598    </OntologyEntry>
599  </DataType_assn>
600      </SpecializedQuantitationType>
601
602      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Comp_Directional_Ratio-Cy5/Cy3" name="Comp_Directional_Ratio-Cy5/Cy3" isBackground="0">
603  <Descriptions_assnlist>
604    <Description text="Compensated directional ratio: if Comp_Ratio &gt; 1 then Directional = Ratio, if Ratio &lt; 1 then Directional = -1/Ratio.">
605    </Description>
606  </Descriptions_assnlist>
607  <Scale_assn>
608    <OntologyEntry category="Scale" value="linear_scale">
609    </OntologyEntry>
610  </Scale_assn>
611  <DataType_assn>
612    <OntologyEntry category="DataType" value="float">
613    </OntologyEntry>
614  </DataType_assn>
615      </SpecializedQuantitationType>
616
617      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Comp_Log2_Ratio" name="Comp_Log2_Ratio" isBackground="0">
618  <Descriptions_assnlist>
619    <Description text="Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3).">
620    </Description>
621  </Descriptions_assnlist>
622  <Scale_assn>
623    <OntologyEntry category="Scale" value="log_base_2">
624    </OntologyEntry>
625  </Scale_assn>
626  <DataType_assn>
627    <OntologyEntry category="DataType" value="float">
628    </OntologyEntry>
629  </DataType_assn>
630      </SpecializedQuantitationType>
631
632      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Comment" name="Comment" isBackground="0">
633  <Descriptions_assnlist>
634    <Description text="Additional description of spot.">
635    </Description>
636  </Descriptions_assnlist>
637  <Scale_assn>
638    <OntologyEntry category="Scale" value="unscaled">
639    </OntologyEntry>
640  </Scale_assn>
641  <DataType_assn>
642    <OntologyEntry category="DataType" value="string_datatype">
643    </OntologyEntry>
644  </DataType_assn>
645      </SpecializedQuantitationType>
646
647      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:SNR-tot" name="SNR-tot" isBackground="1">
648  <Descriptions_assnlist>
649    <Description text="Squared average of Cy5_SNR and Cy3_SNR.">
650    </Description>
651  </Descriptions_assnlist>
652  <Scale_assn>
653    <OntologyEntry category="Scale" value="linear_scale">
654    </OntologyEntry>
655  </Scale_assn>
656  <DataType_assn>
657    <OntologyEntry category="DataType" value="float">
658    </OntologyEntry>
659  </DataType_assn>
660      </SpecializedQuantitationType>
661
662      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:SNR-tot_Score" name="SNR-tot_Score" isBackground="1">
663  <Descriptions_assnlist>
664    <Description text="Squared average of Cy5_%SNR and Cy3_%SNR.">
665    </Description>
666  </Descriptions_assnlist>
667  <Scale_assn>
668    <OntologyEntry category="Scale" value="linear_scale">
669    </OntologyEntry>
670  </Scale_assn>
671  <DataType_assn>
672    <OntologyEntry category="DataType" value="float">
673    </OntologyEntry>
674  </DataType_assn>
675      </SpecializedQuantitationType>
676
677      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:SNR*GS" name="SNR*GS" isBackground="0">
678  <Descriptions_assnlist>
679    <Description text="Number of saturated pixel in both colors (logical or).">
680    </Description>
681  </Descriptions_assnlist>
682  <Scale_assn>
683    <OntologyEntry category="Scale" value="linear_scale">
684    </OntologyEntry>
685  </Scale_assn>
686  <DataType_assn>
687    <OntologyEntry category="DataType" value="float">
688    </OntologyEntry>
689  </DataType_assn>
690      </SpecializedQuantitationType>
691
692      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Replicas" name="Replicas" isBackground="0">
693  <Descriptions_assnlist>
694    <Description text="">
695    </Description>
696  </Descriptions_assnlist>
697  <Scale_assn>
698    <OntologyEntry category="Scale" value="linear_scale">
699    </OntologyEntry>
700  </Scale_assn>
701  <DataType_assn>
702    <OntologyEntry category="DataType" value="float">
703    </OntologyEntry>
704  </DataType_assn>
705      </SpecializedQuantitationType>
706
707      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Regulation" name="Regulation" isBackground="0">
708  <Descriptions_assnlist>
709    <Description text="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.">
710    </Description>
711  </Descriptions_assnlist>
712  <Scale_assn>
713    <OntologyEntry category="Scale" value="unscaled">
714    </OntologyEntry>
715  </Scale_assn>
716  <DataType_assn>
717    <OntologyEntry category="DataType" value="string_datatype">
718    </OntologyEntry>
719  </DataType_assn>
720      </SpecializedQuantitationType>
721
722      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Group name" name="Group name" isBackground="0">
723  <Descriptions_assnlist>
724    <Description text="Group name for this spot.">
725    </Description>
726  </Descriptions_assnlist>
727  <Scale_assn>
728    <OntologyEntry category="Scale" value="unscaled">
729    </OntologyEntry>
730  </Scale_assn>
731  <DataType_assn>
732    <OntologyEntry category="DataType" value="string_datatype">
733    </OntologyEntry>
734  </DataType_assn>
735      </SpecializedQuantitationType>
736
737      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Median of ratios" name="Median of ratios" isBackground="0">
738  <Descriptions_assnlist>
739    <Description text="Median of ratios (Cy5/Cy3) from all pixel in this spot.">
740    </Description>
741  </Descriptions_assnlist>
742  <Scale_assn>
743    <OntologyEntry category="Scale" value="linear_scale">
744    </OntologyEntry>
745  </Scale_assn>
746  <DataType_assn>
747    <OntologyEntry category="DataType" value="float">
748    </OntologyEntry>
749  </DataType_assn>
750      </SpecializedQuantitationType>
751
752      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Median of ratios % SDev" name="Median of ratios % SDev" isBackground="0">
753  <Descriptions_assnlist>
754    <Description text="Standard deviation of Median of ratios in percent.">
755    </Description>
756  </Descriptions_assnlist>
757  <Scale_assn>
758    <OntologyEntry category="Scale" value="linear_scale">
759    </OntologyEntry>
760  </Scale_assn>
761  <DataType_assn>
762    <OntologyEntry category="DataType" value="float">
763    </OntologyEntry>
764  </DataType_assn>
765      </SpecializedQuantitationType>
766
767      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Ratio of medians" name="Ratio of medians" isBackground="0">
768  <Descriptions_assnlist>
769    <Description text="Ratio of Medians (Cy5/Cy3) from all pixel in this spot.">
770    </Description>
771  </Descriptions_assnlist>
772  <Scale_assn>
773    <OntologyEntry category="Scale" value="linear_scale">
774    </OntologyEntry>
775  </Scale_assn>
776  <DataType_assn>
777    <OntologyEntry category="DataType" value="float">
778    </OntologyEntry>
779  </DataType_assn>
780      </SpecializedQuantitationType>
781
782      <SpecializedQuantitationType identifier="EMBL:ChipSkipper_QuantitationType:Ratio of medians % SDev" name="Ratio of medians % SDev" isBackground="0">
783  <Descriptions_assnlist>
784    <Description text="Standard deviation of Ratio of medians in percent.">
785    </Description>
786  </Descriptions_assnlist>
787  <Scale_assn>
788    <OntologyEntry category="Scale" value="linear_scale">
789    </OntologyEntry>
790  </Scale_assn>
791  <DataType_assn>
792    <OntologyEntry category="DataType" value="float">
793    </OntologyEntry>
794  </DataType_assn>
795      </SpecializedQuantitationType>
796
797    </QuantitationType_assnlist>
798  </QuantitationType_package>
799</MAGE-ML>
Note: See TracBrowser for help on using the repository browser.