source: trunk/misc/mage/rawdatatypes/QT_ChipSkipper.xml @ 2925

Last change on this file since 2925 was 2925, checked in by Jari Häkkinen, 16 years ago

Added svndigest:ignore property tom some items.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
  • Property svndigest:ignore set to *
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>
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