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Motivation: Usefulness of analysis derived from Affymetrix microarraysdepends largely upon the reliability of files describing the correspondencebetween probe sets, genes and transcripts. In particular, in case a gene istargeted by two probe sets, one must be able to assess if the correspondingsignals measure a group of common transcripts or two groups of transcripts withlittle or no overlap.  Results: Probe sets that effectively target the same group of transcriptshave specific properties in the trancriptional networks we constructed. Wefound indeed that such probe sets had a very low negative correlation, a highpositive correlation and a similar neighbourhood. Taking advantage of theseproperties, we devised a test allowing to group probe sets which target thesame group of transcripts in a particular network. By considering severalnetworks, additional information concerning the frequency of these associationswas obtained.  Availability and Implementation: The programs developed in Python (PSAWNpy)and in Matlab (PSAWNml) are freely available, and can be downloaded athttp://code.google.com/p/arraymatic/.  Tutorials and reference manuals are available athttp://bns.crbm.cnrs.fr/softwares.html.  Contact: mbellis@crbm.cnrs.fr.  Supplementary information: Supplementary data are available athttp://bns.crbm.cnrs.fr/download.html.

Mapping of Affymetrix probe sets to groups of transcripts using transcriptional networks