source: plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationWA.base @ 2015

Last change on this file since 2015 was 2015, checked in by olle, 9 years ago

Refs #84. ReplicateError BASE1 plug-in configuration file lib/pluginConfigurationWA.base updated in parameter info, as the previous update erroneously included parameters used by ReplicateErrorAA, but not by ReplicateErrorWA.

  • Property svn:eol-style set to native
File size: 1.6 KB
Line 
1BASEfile
2section plugin
3uniqueName  onk.lu.se/enell/ReplicateError
4versionNumber @VERSION@
5name  Filter: ReplicateError (within assays)
6descr Implementation of 'Analysis of replicates' (cf. figure 4 in the publication)\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.\r\n\r\nParameters:\r\n\r\nStandard deviation limit - Filters out values outside the limit. A limit value <= 0 indicates that no limit is used.\r\n\r\nLeave singletons - Flag indicating if spots occurring once should be leaved.\r\n\r\nCenter of mass - median (default) or mean
7execName  runWA
8geneAverages  0
9serialFormat  0
10url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12429061
11minChannels 2
12maxChannels 0
13leaveStdin  0
14leaveStdout 0
15estimatedTime 60
16defaultMaxRam 67108864
17usedColumns position\treporter
18usedFields  _allIntensities
19columns position  valueType name  commonName  options defaultValue  enumOptions removed
20%
211 e strictReplicate Replicate filter  30  true  true\ton\tfalse\toff  1
222 h section   30  settings    0
233 f sdLimit Standard deviation limit  30  2.0   0
244 e newBAS  Create new bioassay set 30  true  true\tyes\tfalse\tno  1
255 e leaveSingletons Leave singletons  30  false true\tyes\tfalse\tno  0
266 e leaveDataFiles  Put gnuplot file in zip archive 30  false true\tyes\tfalse\tno  1
277 e method  Method  30  1 1\tSD Limit\t2\tmin(ch1, ch2)\t3\t### 1
288 f startvalue  Start value 30      1
299 f stepSize  Step size 30      1
3010  f rTarget R target  30  0.95    1
3111  e center  Center of mass  30  0 0\tMedian\t1\tMean  0
32
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