source: plugins/base2/net.sf.basedb.agilent/trunk/config/agilent-raw-data-types.xml @ 1199

Last change on this file since 1199 was 1199, checked in by Jari Häkkinen, 12 years ago

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1<?xml version="1.0" encoding="UTF-8" ?>
2<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
3<!--
4  $Id: agilent-raw-data-types.xml 1199 2010-03-06 08:54:15Z jari $
5
6  Copyright (C) 2010 Jari Häkkinen
7
8  This file is part of the Agilent plug-in package for BASE
9  (net.sf.based.agilent).
10  The package is available at http://baseplugins.thep.lu.se/
11  BASE main site is http://base.thep.lu.se/
12
13  This is free software; you can redistribute it and/or modify it
14  under the terms of the GNU General Public License as published by
15  the Free Software Foundation; either version 3 of the License, or
16  (at your option) any later version.
17
18  The software is distributed in the hope that it will be useful, but
19  WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21  General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with this program. If not, see <http://www.gnu.org/licenses/>.
25-->
26
27<raw-data-types>
28
29  <raw-data-type
30    id="agilent1ch"
31    channels="1"
32    name="AgilentGE1ch"
33    table="RawDataAgilent1ch"
34    >
35    <property
36      name="gSurrogateUsed"
37      title="G surrogate used"
38      description="The green surrogate value used."
39      column="g_surrogate_used"
40      channel="1"
41      type="float"
42      averagemethod="none"
43    />
44    <property
45      name="gIsFound"
46      title="G is found"
47      description="A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NOTE: IsFound was previously termed IsStrong."
48      column="g_is_found"
49      channel="1"
50      type="boolean"
51      averagemethod="none"
52    />
53    <property
54      name="gProcessedSignal"
55      title="G processed signal"
56      description="The propagated feature signal, per channel, used for computation of log ratio."
57      column="g_processed_signal"
58      channel="1"
59      type="float"
60      averagemethod="arithmetic_mean"
61    />
62    <property
63      name="gNumPixOLHi"
64      title="G high outlier pixels"
65      description="Number of outlier pixels per feature with intensity &gt; 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."
66      column="g_high_outlier_pixels"
67      channel="1"
68      type="int"
69      averagemethod="arithmetic_mean"
70    />
71    <property
72      name="gNumPixOLLo"
73      title="G low outlier pixels"
74      description="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."
75      column="g_low_outlier_pixels"
76      channel="1"
77      type="int"
78      averagemethod="arithmetic_mean"
79    />
80    <property
81      name="gNumPix"
82      title="G pixels"
83      description="Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels."
84      column="g_pixels"
85      channel="1"
86      type="int"
87      averagemethod="arithmetic_mean"
88    />
89    <property
90      name="gMeanSignal"
91      title="G mean signal"
92      description="Raw mean signal of feature in green channel."
93      column="g_mean_signal"
94      channel="1"
95      type="float"
96      averagemethod="arithmetic_mean"
97    />
98    <property
99      name="gMedianSignal"
100      title="G median signal"
101      description="Raw median signal of feature in green channel."
102      column="g_median_signal"
103      channel="1"
104      type="float"
105      averagemethod="arithmetic_mean"
106    />
107    <property
108      name="gBGNumPix"
109      title="G background pixels"
110      description="Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel."
111      column="g_bg_pixels"
112      channel="1"
113      type="int"
114      averagemethod="arithmetic_mean"
115    />
116    <property
117      name="gBGMeanSignal"
118      title="G mean background"
119      description="Mean local background signal (local to corresponding feature) computed per channel."
120      column="g_bg_mean_signal"
121      channel="1"
122      type="float"
123      averagemethod="arithmetic_mean"
124    />
125    <property
126      name="gBGMedianSignal"
127      title="G median background"
128      description="Median local background signal (local to corresponding feature) computed per channel."
129      column="g_bg_median_signal"
130      channel="1"
131      type="float"
132      averagemethod="arithmetic_mean"
133    />
134    <property
135      name="gNumSatPix"
136      title="G saturated pixels"
137      description="Total number of saturated pixels per feature, computed per channel."
138      column="g_sat_pixels"
139      channel="1"
140      type="int"
141      averagemethod="arithmetic_mean"
142    />
143    <property
144      name="gIsSaturated"
145      title="G is saturated"
146      description="Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated."
147      column="g_is_saturated"
148      channel="1"
149      type="boolean"
150      averagemethod="none"
151    />
152    <property
153      name="gIsFeatNonUnifOL"
154      title="G non-uniform outlier"
155      description="Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
156      column="g_nonuniform_outlier"
157      channel="1"
158      type="boolean"
159      averagemethod="none"
160    />
161    <property
162      name="gIsBGNonUnifOL"
163      title="G bg non-uniform outlier"
164      description="Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a 'uniform' feature. A 1 indicates Feature is a non-uniformity outlier."
165      column="g_bg_nonuniform_outlier"
166      channel="1"
167      type="boolean"
168    />
169    <property
170      name="gIsFeatPopnOL"
171      title="G population outlier"
172      description="Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates Feature is a population outlier."
173      column="g_population_outlier"
174      channel="1"
175      type="boolean"
176    />
177    <property
178      name="gIsBGPopnOL"
179      title="G bg population outlier"
180      description="Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (i.e. IQR) of the population. A 1 indicates background is a population outlier."
181      column="g_bg_population_outlier"
182      channel="1"
183      type="boolean"
184      averagemethod="none"
185    />
186    <property
187      name="IsManualFlag"
188      title="Manual flag"
189      description="If a feature has been moved manually this flag will be set to 1."
190      column="manual_flag"
191      type="boolean"
192      averagemethod="none"
193    />
194    <property
195      name="gBGSubSignal"
196      title="G net signal"
197      description="The net green signal following the subtraction of the background from the raw mean green signal."
198      column="g_net_signal"
199      channel="1"
200      type="float"
201    />
202    <property
203      name="gIsPosAndSignif"
204      title="G > 0 and significant"
205      description="Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature is positive and significant above background."
206      column="g_significant"
207      channel="1"
208      type="boolean"
209      averagemethod="none"
210    />
211    <property
212      name="gPValFeatEqBG"
213      title="G p-value"
214      description="P-value from t-test of significance between green Mean signal and green background."
215      column="g_pvalue"
216      channel="1"
217      type="float"
218      averagemethod="none"
219    />
220    <property
221      name="gNumBGUsed"
222      title="G background pixels"
223      description="A count of the number of background pixels used in the green channel."
224      column="g_numbg_used"
225      channel="1"
226      type="int"
227      averagemethod="arithmetic_mean"
228    />
229    <property
230      name="gIsWellAboveBG"
231      title="G well above bg"
232      description="Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG."
233      column="g_above_bg"
234      channel="1"
235      type="boolean"
236      averagemethod="none"
237    />
238    <property
239      name="gBGUsed"
240      title="G bg used"
241      description="Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel."
242      column="g_bg_used"
243      channel="1"
244      type="float"
245      averagemethod="arithmetic_mean"
246    />
247    <property
248      name="ErrorModel"
249      title="Error model"
250      description="ErrorModel Indicates the error model that the user chose for feature extraction. A 0 indicates use of the Propogated Error Model. A 1 indicates use of the Universal Error Model."
251      column="error_model"
252      type="int"
253      averagemethod="none"
254    />
255    <property
256      name="gSpatialDetrendIsInFilteredSet"
257      title="G spatial trend"
258      description="Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features."
259      column="g_spatial_trend"
260      channel="1"
261      type="boolean"
262      averagemethod="none"
263    />
264    <property
265      name="gSpatialDetrendSurfaceValue"
266      title="G surface value"
267      description="Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet."
268      column="g_surface_value"
269      channel="1"
270      type="float"
271      averagemethod="arithmetic_mean"
272    />
273    <property
274       name="gPixSDev"
275       title="G pixel SDev"
276       description="Standard deviation of all inlier pixels per feature; this is computed independently in each channel."
277       column="gPixSDev"
278       type="float"
279       averagemethod="none"
280     />
281    <property
282       name="gBGPixSDev"
283       title="G background pixel SDev"
284       description="Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channelStandard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel."
285       column="gBGPixSDev"
286       type="float"
287       averagemethod="none"
288    />
289    <intensity-formula
290      name="mean"
291      title="Mean FG - Mean BG"
292      description="Subtract mean background from mean foreground"
293      >
294      <formula channel="1"
295               expression="raw('gMeanSignal') - raw('gBGMeanSignal')" />
296    </intensity-formula>
297    <intensity-formula
298      name="median"
299      title="Median FG - Median BG"
300      description="Subtract meadian background from median foreground"
301      >
302      <formula channel="1"
303               expression="raw('gMedianSignal') - raw('gBGMedianSignal')" />
304    </intensity-formula>
305    <intensity-formula
306      name="medianmean"
307      title="Median FG - Mean BG"
308      description="Subtract mean background from median foreground"
309      >
310      <formula channel="1"
311               expression="raw('gMedianSignal') - raw('gBGMeanSignal')" />
312    </intensity-formula>
313    <intensity-formula
314      name="meanmedian"
315      title="Mean FG - Median BG"
316      description="Subtract median background from mean foreground"
317      >
318      <formula channel="1"
319               expression="raw('gMeanSignal') - raw('gBGMedianSignal')" />
320    </intensity-formula>
321    <intensity-formula
322      name="meanfg"
323      title="Mean FG"
324      description="Mean foreground"
325      >
326      <formula channel="1"
327               expression="raw('gMeanSignal')" />
328    </intensity-formula>
329    <intensity-formula
330      name="medianfg"
331      title="Median FG"
332      description="Median foreground"
333      >
334      <formula channel="1"
335               expression="raw('gMedianSignal')" />
336    </intensity-formula>
337    <intensity-formula
338      name="medianfgmeanmedianbg"
339      title="Median FG - Mean(Median BG)"
340      description="Subtract mean of median backgrounds from median foreground"
341      >
342      <formula channel="1"
343               expression="raw('gMedianSignal') - mean('gBGMedianSignal')" />
344    </intensity-formula>
345    <intensity-formula
346      name="meanfgmeanmeanbg"
347      title="Mean FG - Mean(Mean BG)"
348      description="Subtract mean of mean backgrounds from mean foreground"
349      >
350      <formula channel="1"
351               expression="raw('gMeanSignal') - mean('gBGMeanSignal')"  />
352    </intensity-formula>
353    <intensity-formula
354      name="medianfgmeanmeanbg"
355      title="Median FG - Mean(Mean BG)"
356      description="Subtract mean of mean backgrounds from median foreground"
357      >
358      <formula channel="1"
359        expression="raw('gMedianSignal') - mean('gBGMeanSignal')" />
360    </intensity-formula>
361    <intensity-formula
362      name="meanfgmeanmedianbg"
363      title="Mean FG - Mean(Median BG)"
364      description="Subtract mean of median backgrounds from mean foreground"
365      >
366      <formula channel="1"
367               expression="raw('gMeanSignal') - mean('gBGMedianSignal')" />
368    </intensity-formula>
369  </raw-data-type>
370
371</raw-data-types>
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