Dear Kripa, Short answer: If you really must average over multiple probes for a given gene, then the limma function you are looking for is avereps(). Longer answer: This question has come up a few times recently on this mailing list, and I wonder whether you and other posters might be thinking of summarization as is done by the RMA algorithm for Affymetrix arrays over multiple probes in a probe-set. The equivalent of this for an Illumina BeadChip is to summarize the multiple beads for each probe on each array. This step is done by the Illumina Genome Studio software, so has already been completed before entry into limma. On the other hand, summarizing multiple probes for a given gene (or multiple probe-sets for an Affy array) is not recommended as a routine procedure by any of the Bioconductor software developers. The whole reason that multiple probes are provided by Illumina for a given gene is that the gene may take different isoforms to which the different probes may respond. Why would you want to lose this information by pre- emptively averaging? Best wishes Gordon > Date: Fri, 9 Mar 2012 21:42:58 +0000 > From: Kripa R <kripa777 at="" hotmail.com=""> > To: <bioconductor at="" r-project.org=""> > Subject: [BioC] LIMMA - summarization > > Hi everyone, > I'm working on an analysis of illumina microarrays and am using the > limma package. But looking at the code provided with the vignette there > doesn't seem to be a summarization step (where multiple probes for the > same gene are combined) > Am I missing something here or would I need to use a different package > to summarize (ie beadarray or lumi)? > > Thanks, > > > -Kripa ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Yes, I see what you mean; each illumina probe provides unique information. I guess all the affy summarization options threw me off (avgdiff, liwong, mas, medianpolish, playerout) One thing, the avereps function would be looking for identical ProbeID but would it be possible to change this to look for identical gene names/ look for replicates using a different column? Thanks > Date: Mon, 12 Mar 2012 09:09:15 +1100 > From: smyth@wehi.EDU.AU > To: kripa777@hotmail.com > CC: bioconductor@r-project.org > Subject: LIMMA - summarization of Illumina probes for same gene > > Dear Kripa, > > Short answer: > > If you really must average over multiple probes for a given gene, then the > limma function you are looking for is avereps(). > > Longer answer: > > This question has come up a few times recently on this mailing list, and I > wonder whether you and other posters might be thinking of summarization as > is done by the RMA algorithm for Affymetrix arrays over multiple probes > in a probe-set. The equivalent of this for an Illumina BeadChip is to > summarize the multiple beads for each probe on each array. This step is > done by the Illumina Genome Studio software, so has already been completed > before entry into limma. > > On the other hand, summarizing multiple probes for a given gene (or > multiple probe-sets for an Affy array) is not recommended as a routine > procedure by any of the Bioconductor software developers. The whole > reason that multiple probes are provided by Illumina for a given gene is > that the gene may take different isoforms to which the different probes > may respond. Why would you want to lose this information by pre- emptively > averaging? > > Best wishes > Gordon > > > Date: Fri, 9 Mar 2012 21:42:58 +0000 > > From: Kripa R <kripa777@hotmail.com> > > To: <bioconductor@r-project.org> > > Subject: [BioC] LIMMA - summarization > > > > Hi everyone, > > > I'm working on an analysis of illumina microarrays and am using the > > limma package. But looking at the code provided with the vignette there > > doesn't seem to be a summarization step (where multiple probes for the > > same gene are combined) > > > Am I missing something here or would I need to use a different package > > to summarize (ie beadarray or lumi)? > > > > Thanks, > > > > > > -Kripa > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:9}}