Hi bioconductor mailing list, I got a (another) problem with redundant probesets from Affymetrix chips: For my downstream analysis to work, I need only 1 expression value per gene (eg Entrez Id). So by now I have a table that looks something like this: N probe set gene id expression 1 *12345_at* *123* 1.5 2 123456_at 1234 2 3 *1234567_at* *123* 1.6 4 12345678_at 12345 4 5 *123456789_at* *123* 1.4 By collapsing I mean as a result something like this: N probe set gene id expression 1 *12345_at* *123* *1.5* <= eg median 2 123456_at 1234 2 4 12345678_at 12345 4 I hope one can help me out! I have seen this in several publications, so there must be a way. Thanks in advance, Andreas Heider [[alternative HTML version deleted]]

Hi Andreas, Try the function avereps in limma. Mete -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Andreas Heider Sent: Thursday, April 28, 2011 2:13 AM To: bioconductor at r-project.org Subject: [BioC] collapsing redundant probe sets of Affymetrix Chips Hi bioconductor mailing list, I got a (another) problem with redundant probesets from Affymetrix chips: For my downstream analysis to work, I need only 1 expression value per gene (eg Entrez Id). So by now I have a table that looks something like this: N probe set gene id expression 1 *12345_at* *123* 1.5 2 123456_at 1234 2 3 *1234567_at* *123* 1.6 4 12345678_at 12345 4 5 *123456789_at* *123* 1.4 By collapsing I mean as a result something like this: N probe set gene id expression 1 *12345_at* *123* *1.5* <= eg median 2 123456_at 1234 2 4 12345678_at 12345 4 I hope one can help me out! I have seen this in several publications, so there must be a way. Thanks in advance, Andreas Heider [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor IMPORTANT WARNING: This email (and any attachments) is ...{{dropped:9}}