Changeset 1093 for plugins/base2/net.sf.basedb.illumina/trunk/README

Timestamp:

May 27, 2009, 2:16:32 PM (14 years ago)

Author:

Martin Svensson

Message:

References #182 The information is now inserted in the README file, in the section about Illumina Bead Summary (IBS) files.

File:

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

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

@@ -91 +91 @@
  - ''' Mean GRN ''': The mean intensity.
  - ''' Dev GRN ''': Standard deviation of the mean intensity. 
+
+IBS files may contain some rows with Illumicodes that are not represented in the 
+BGX files. 
+Our interpretation is that some probes that used to be annotated with a gene has 
+later been considered poor by Illumina (as we have only observed an increase 
+in the number of unmatched probes for later bgx revisions). To avoid that the 
+raw data importer fails cause of some probes, listed in the IBS-file, couldn't 
+be found in BASE - you have to set plug-in parameter 'Probe not found=skip', 
+when importing data from an IBS-file into BASE.
 
 A new raw data type has been defined in illumina-raw-data-types.xml