Changeset 1203

Timestamp:

Mar 11, 2010, 11:30:14 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Improved documentation for Background correction plug-in

Location:

plugins/base2/net.sf.basedb.illumina/trunk

Files:

• README_PluginDetails (modified) (5 diffs)
• src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java (modified) (1 diff)

plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

@@ -5 +5 @@
 There are many plug-ins in the Illumina plug-in package for BASE. This
 file gives detailed information on some of the contributed plug-ins.
+
+
+== Illumina expression background correction plug-in ==
+
+This plug-in will remove a per-slide global background from all
+spots. The background is calculated from a set of negative control
+spot on the array. See implementation details below for details.
+
+=== Parameters ===
+
+The only parameter to set is how background intensities should be
+calculated. Allowed values are median or mean, i.e. the background is
+either the median or the mean of the negative control spots on the
+array.
+
+=== Implementation details ===
+
+Each assay is treated separately, i.e., no samples are combined
+together. All calculations are made on the current bioassay data
+implying that this plug-in should be used early in analysis and before
+background spots are removed.
+
+A spot is considered to be a negative control spot if it has an
+''Control group name'' exactly matching the string ''negative''.
+
 
 
@@ -25 +50 @@
 plug-in.
 
-
 === Parameters ===
 
@@ -42 +66 @@
 }}}
 where `MAD` is the median absolute deviation.
-
 
 === Implementation details ===
@@ -70 +93 @@
 value for arguments outside this range is set to -1 and 1,
 respectively.
+
 
 
@@ -100 +124 @@
 ----------------------------------------------------------------------
 {{{
-Copyright (C) 2009 Jari Häkkinen
+Copyright (C) 2009, 2010 Jari Häkkinen
 
 This file is part of Illumina plug-in package for BASE.

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java

@@ -91 +91 @@
   private static final About about = new AboutImpl
     ( "Illumina expression background correction", 
-      "This plug-in implements BeadStudio like background correction methods " +
-      "for Illumina expression data. Please send feedback to " +
+      "This plug-in will remove a per-slide global background from all " +
+      "spots. The background is calculated from a set of negative control " +
+      "spots on the array.\n\n" +
+      "Each assay is treated separately, i.e., no samples are combined " +
+      "together. All calculations are made on the current bioassay data " +
+      "implying that this plug-in should be used early in analysis and before " +
+      "background spots are removed.\n\n" +
+      "A spot is considered to be a negative control spot if it has an " +
+      "''Control group name'' exactly matching the string ''negative''.\n\n" +
+      "The only parameter to set is how background intensities should be " +
+      "calculated. Allowed values are median or mean, i.e. the background is " +
+      "either the median or the mean of the negative control spots on the " +
+      "array.\n\n" +
+      "Please send feedback to " +
       Illumina.EMAIL,
       Illumina.VERSION,