Changeset 1179 for plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

Timestamp:

Oct 21, 2009, 12:09:42 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #251.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails (modified) (1 diff)

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

@@ -72 +72 @@
 
 
+== Control Summary plots ==
+
+This package provides overview plots for Illumina expression data. The
+'Overview plots' tab becomes available in the experiment analysis tree
+when the user selects a bioassay set. The plots are automatically
+generated when the user clicks on the Overview plots tab. The display
+of the plots cannot be changed by the user and the same plot is shown
+irrespective which bioassay set is selected.
+
+Currently two control summary curves are generated in one plot; The
+average intensity of perfect match beads in each assay, and the
+average intensity of housekeeping beads in each assay.
+
+The average intensity I_avg is calculated as
+
+    I_avg = sum[Iraw_i] / N
+
+where N is the number of bead types in the sum, Iraw_i is the raw
+mean intensity for bead type i.
+
+A bead type is considered to belong to the perfect match group if it
+is annotated with ':pm' in the reporter annotation column '[Rep]
+Control group id', and a bead type is grouped as housekeeping if it is
+annotated with 'housekeeping' in reporter annotator column '[Rep]
+Control group id'.
+
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