source: trunk/misc/mage/rawdatatypes/QT_Spotfinder.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: 12.2 KB
Line 
1<?xml version="1.0" encoding="ISO-8859-1" 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="EBI:eleh:Spotfinder QT XML">
5  <QuantitationType_package>
6    <QuantitationType_assnlist>
7      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:R" name="R" isBackground="false">
8  <Descriptions_assnlist>
9    <Description text="Spot row number in slide.">
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      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:C" name="C" isBackground="false">
22  <Descriptions_assnlist>
23    <Description text="Spot column number in slide.">
24    </Description>
25  </Descriptions_assnlist>
26  <Scale_assn>
27    <OntologyEntry category="Scale" value="unscaled">
28    </OntologyEntry>
29  </Scale_assn>
30  <DataType_assn>
31    <OntologyEntry category="DataType" value="integer">
32    </OntologyEntry>
33  </DataType_assn>
34      </SpecializedQuantitationType>
35      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:MR" name="MR" isBackground="false">
36  <Descriptions_assnlist>
37    <Description text="Spot metarow number or subrow number.">
38    </Description>
39  </Descriptions_assnlist>
40  <Scale_assn>
41    <OntologyEntry category="Scale" value="unscaled">
42    </OntologyEntry>
43  </Scale_assn>
44  <DataType_assn>
45    <OntologyEntry category="DataType" value="integer">
46    </OntologyEntry>
47  </DataType_assn>
48      </SpecializedQuantitationType>
49      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:MC" name="MC" isBackground="false">
50  <Descriptions_assnlist>
51    <Description text="Spot metacolumn number or subcolumn number.">
52    </Description>
53  </Descriptions_assnlist>
54  <Scale_assn>
55    <OntologyEntry category="Scale" value="unscaled">
56    </OntologyEntry>
57  </Scale_assn>
58  <DataType_assn>
59    <OntologyEntry category="DataType" value="integer">
60    </OntologyEntry>
61  </DataType_assn>
62      </SpecializedQuantitationType>
63      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SR" name="SR" isBackground="false">
64  <Descriptions_assnlist>
65    <Description text="Spot row number in a block/grid.">
66    </Description>
67  </Descriptions_assnlist>
68  <Scale_assn>
69    <OntologyEntry category="Scale" value="unscaled">
70    </OntologyEntry>
71  </Scale_assn>
72  <DataType_assn>
73    <OntologyEntry category="DataType" value="integer">
74    </OntologyEntry>
75  </DataType_assn>
76      </SpecializedQuantitationType>
77      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SC" name="SC" isBackground="false">
78  <Descriptions_assnlist>
79    <Description text="Spot column number in a block/grid.">
80    </Description>
81  </Descriptions_assnlist>
82  <Scale_assn>
83    <OntologyEntry category="Scale" value="unscaled">
84    </OntologyEntry>
85  </Scale_assn>
86  <DataType_assn>
87    <OntologyEntry category="DataType" value="integer">
88    </OntologyEntry>
89  </DataType_assn>
90      </SpecializedQuantitationType>
91      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:IA" name="IA" isBackground="false">
92  <Descriptions_assnlist>
93    <Description text="Spot intensity in channel A corrected for background.">
94    </Description>
95  </Descriptions_assnlist>
96  <Channel_assnref>
97    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
98  </Channel_assnref>
99  <Scale_assn>
100    <OntologyEntry category="Scale" value="linear_scale">
101    </OntologyEntry>
102  </Scale_assn>
103  <DataType_assn>
104    <OntologyEntry category="DataType" value="integer">
105    </OntologyEntry>
106  </DataType_assn>
107      </MeasuredSignal>
108      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:IB" name="IB" isBackground="false">
109  <Descriptions_assnlist>
110    <Description text="Spot intensity in channel B corrected for background.">
111    </Description>
112  </Descriptions_assnlist>
113  <Channel_assnref>
114    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
115  </Channel_assnref>
116  <Scale_assn>
117    <OntologyEntry category="Scale" value="linear_scale">
118    </OntologyEntry>
119  </Scale_assn>
120  <DataType_assn>
121    <OntologyEntry category="DataType" value="integer">
122    </OntologyEntry>
123  </DataType_assn>
124      </MeasuredSignal>
125      <Ratio identifier="TIGR:Spotfinder_QuantitationType:MeanR" name="MeanR" isBackground="false">
126  <Descriptions_assnlist>
127    <Description text="Spot mean ratio.">
128    </Description>
129  </Descriptions_assnlist>
130  <Scale_assn>
131    <OntologyEntry category="Scale" value="linear_scale">
132    </OntologyEntry>
133  </Scale_assn>
134  <DataType_assn>
135    <OntologyEntry category="DataType" value="float">
136    </OntologyEntry>
137  </DataType_assn>
138      </Ratio>
139      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SA" name="SA" isBackground="false">
140  <Descriptions_assnlist>
141    <Description text="Spot total area in pixels.">
142    </Description>
143  </Descriptions_assnlist>
144  <Scale_assn>
145    <OntologyEntry category="Scale" value="linear_scale">
146    </OntologyEntry>
147  </Scale_assn>
148  <DataType_assn>
149    <OntologyEntry category="DataType" value="integer">
150    </OntologyEntry>
151  </DataType_assn>
152      </SpecializedQuantitationType>
153      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:Sat" name="Sat" isBackground="false">
154  <Descriptions_assnlist>
155    <Description text="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration.">
156    </Description>
157  </Descriptions_assnlist>
158  <Scale_assn>
159    <OntologyEntry category="Scale" value="linear_scale">
160    </OntologyEntry>
161  </Scale_assn>
162  <DataType_assn>
163    <OntologyEntry category="DataType" value="float">
164    </OntologyEntry>
165  </DataType_assn>
166      </SpecializedQuantitationType>
167      <Ratio identifier="TIGR:Spotfinder_QuantitationType:MedianR" name="MedianR" isBackground="false">
168  <Descriptions_assnlist>
169    <Description text="Spot median ratio.">
170    </Description>
171  </Descriptions_assnlist>
172  <Scale_assn>
173    <OntologyEntry category="Scale" value="linear_scale">
174    </OntologyEntry>
175  </Scale_assn>
176  <DataType_assn>
177    <OntologyEntry category="DataType" value="float">
178    </OntologyEntry>
179  </DataType_assn>
180      </Ratio>
181      <Ratio identifier="TIGR:Spotfinder_QuantitationType:ModeR" name="ModeR" isBackground="false">
182  <Descriptions_assnlist>
183    <Description text="Spot mode ratio.">
184    </Description>
185  </Descriptions_assnlist>
186  <Scale_assn>
187    <OntologyEntry category="Scale" value="linear_scale">
188    </OntologyEntry>
189  </Scale_assn>
190  <DataType_assn>
191    <OntologyEntry category="DataType" value="float">
192    </OntologyEntry>
193  </DataType_assn>
194      </Ratio>
195      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:BGA" name="BGA" isBackground="true">
196  <Descriptions_assnlist>
197    <Description text="Spot background in channel A.">
198    </Description>
199  </Descriptions_assnlist>
200  <Channel_assnref>
201    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
202  </Channel_assnref>
203  <Scale_assn>
204    <OntologyEntry category="Scale" value="linear_scale">
205    </OntologyEntry>
206  </Scale_assn>
207  <DataType_assn>
208    <OntologyEntry category="DataType" value="integer">
209    </OntologyEntry>
210  </DataType_assn>
211      </MeasuredSignal>
212      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:BGB" name="BGB" isBackground="true">
213  <Descriptions_assnlist>
214    <Description text="Spot background in channel B.">
215    </Description>
216  </Descriptions_assnlist>
217  <Channel_assnref>
218    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
219  </Channel_assnref>
220  <Scale_assn>
221    <OntologyEntry category="Scale" value="linear_scale">
222    </OntologyEntry>
223  </Scale_assn>
224  <DataType_assn>
225    <OntologyEntry category="DataType" value="integer">
226    </OntologyEntry>
227  </DataType_assn>
228      </MeasuredSignal>
229      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:FlagA" name="FlagA" isBackground="false">
230  <Descriptions_assnlist>
231    <Description text="Spot flag in channel A. This flag is set by QC filter.">
232    </Description>
233  </Descriptions_assnlist>
234  <Channel_assnref>
235    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
236  </Channel_assnref>
237  <Scale_assn>
238    <OntologyEntry category="Scale" value="unscaled">
239    </OntologyEntry>
240  </Scale_assn>
241  <DataType_assn>
242    <OntologyEntry category="DataType" value="string_datatype">
243    </OntologyEntry>
244  </DataType_assn>
245      </SpecializedQuantitationType>
246      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:FlagB" name="FlagB" isBackground="false">
247  <Descriptions_assnlist>
248    <Description text="Spot flag in channel B. This flag is set by QC filter.">
249    </Description>
250  </Descriptions_assnlist>
251  <Channel_assnref>
252    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
253  </Channel_assnref>
254  <Scale_assn>
255    <OntologyEntry category="Scale" value="unscaled">
256    </OntologyEntry>
257  </Scale_assn>
258  <DataType_assn>
259    <OntologyEntry category="DataType" value="string_datatype">
260    </OntologyEntry>
261  </DataType_assn>
262      </SpecializedQuantitationType>
263      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QCA" name="QCA" isBackground="false">
264  <Descriptions_assnlist>
265    <Description text="Spot QC score in channel A. This is a geometric mean of shape and S/N QC scores in channel A. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1.">
266    </Description>
267  </Descriptions_assnlist>
268  <Channel_assnref>
269    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
270  </Channel_assnref>
271  <Scale_assn>
272    <OntologyEntry category="Scale" value="linear_scale">
273    </OntologyEntry>
274  </Scale_assn>
275  <DataType_assn>
276    <OntologyEntry category="DataType" value="float">
277    </OntologyEntry>
278  </DataType_assn>
279      </SpecializedQuantitationType>
280      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QCB" name="QCB" isBackground="false">
281  <Descriptions_assnlist>
282    <Description text="Spot QC score in channel B. This is a geometric mean of shape and S/N QC scores in channel B. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1.">
283    </Description>
284  </Descriptions_assnlist>
285  <Channel_assnref>
286    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
287  </Channel_assnref>
288  <Scale_assn>
289    <OntologyEntry category="Scale" value="linear_scale">
290    </OntologyEntry>
291  </Scale_assn>
292  <DataType_assn>
293    <OntologyEntry category="DataType" value="float">
294    </OntologyEntry>
295  </DataType_assn>
296      </SpecializedQuantitationType>
297      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QC" name="QC" isBackground="false">
298  <Descriptions_assnlist>
299    <Description text="Spot total QC score. This is a mean of QC scores in channels A and B.">
300    </Description>
301  </Descriptions_assnlist>
302  <Scale_assn>
303    <OntologyEntry category="Scale" value="linear_scale">
304    </OntologyEntry>
305  </Scale_assn>
306  <DataType_assn>
307    <OntologyEntry category="DataType" value="float">
308    </OntologyEntry>
309  </DataType_assn>
310      </SpecializedQuantitationType>
311      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:Flag" name="Flag" isBackground="false">
312  <Descriptions_assnlist>
313    <Description text="Flag values are generated based on next conditions: A - the number of non-saturated pixels in spot is 0; B- number of non-saturated pixels in spot is between 30 and 50; C- number of non saturated pixels in spot is more then 50; S- fully or partially saturated spot, this is a warning flag. User should evaluate used spot area. X- spot was detected and rejected based on spot shape and spot intensity relative to surrounding background; Z- spot was not detected by the program; Y- spot background is higher than spot intensity.">
314    </Description>
315  </Descriptions_assnlist>
316  <Scale_assn>
317    <OntologyEntry category="Scale" value="unscaled">
318    </OntologyEntry>
319  </Scale_assn>
320  <DataType_assn>
321    <OntologyEntry category="DataType" value="string_datatype">
322    </OntologyEntry>
323  </DataType_assn>
324      </SpecializedQuantitationType>
325    </QuantitationType_assnlist>
326  </QuantitationType_package>
327</MAGE-ML>
Note: See TracBrowser for help on using the repository browser.