Changeset 2013

Timestamp:

Aug 1, 2013, 4:08:29 PM (9 years ago)

Author:

olle

Message:

Fixes #84. ReplicateError BASE1 plug-in configuration files lib/pluginConfigurationAA.base and lib/pluginConfigurationWA.base updated with info on parameters; specifically that a value of sdLimit <= 0 corresponds to unlimited standard deviation, i.e. no filtering is performed based on the standard deviation.

Location:

plugins/base1/se.lu.onk.ReplicateError/trunk/lib

Files:

• pluginConfigurationAA.base (modified) (1 diff)
• pluginConfigurationWA.base (modified) (1 diff)

plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationAA.base

@@ -4 +4 @@
 versionNumber @VERSION@
 name  Filter: ReplicateError (across assays)
-descr Implementation of 'Analysis of replicates' (cf. figure 5 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.
+descr Implementation of 'Analysis of replicates' (cf. figure 5 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\nassayname - Name of assay.\r\n\r\nGroup\r\n\r\nSort\r\n\r\nCenter of mass - median (default) or mean\r\n\r\nAssays to include
 execName  runAA
 geneAverages  0

plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationWA.base

@@ -4 +4 @@
 versionNumber @VERSION@
 name  Filter: ReplicateError (within assays)
-descr 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.
+descr 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\nassayname - Name of assay.\r\n\r\nGroup\r\n\r\nSort\r\n\r\nCenter of mass - median (default) or mean\r\n\r\nAssays to include
 execName  runWA
 geneAverages  0