[BioC] Affy: probeset to gene expression with expresso

[Martin Preusse]

Thanks! This clarifies everything ;) I misunderstood the 'summary' part of expresso. 



Am Dienstag, 13. August 2013 um 17:41 schrieb James W. MacDonald:

> Hi Martin,
> 
> None of the functions in the affy package know anything about the 
> annotation of the various probesets, so there is no facility there to 
> summarize at anything but the probeset level.
> 
> However, you could use one of the MBNI remapped probesets, which 
> pre-aggregate the probes into probesets based on a few different 
> annotation databases.
> 
> Best,
> 
> Jim
> 
> 
> 
> On 8/13/2013 11:38 AM, Martin Preusse wrote:
> > Hi Jim,
> > 
> > thanks, this is a very clever (and R like) way to average the expressions on the expression matrix. In my example this would work for 'exprs(eset)' when I replace the probe set ids with gene symbols.
> > 
> > Still, it would be great to know if can be achieved with a convenience function (e.g. expresso).
> > 
> > Martin
> > 
> > 
> > Am Dienstag, 13. August 2013 um 17:28 schrieb James W. MacDonald:
> > 
> > > Hi Martin,
> > > 
> > > I just answered a very closely related question. See if this helps:
> > > 
> > > https://stat.ethz.ch/pipermail/bioconductor/2013-August/054353.html
> > > 
> > > Best,
> > > 
> > > Jim
> > > 
> > > 
> > > 
> > > On 8/13/2013 9:47 AM, Martin Preusse wrote:
> > > > I am trying to get the gene level expression values from an Affy micro array, i.e. merge the values for probe sets representing the same gene.
> > > > 
> > > > I tried to use the 'expresso' function from the affy package, but I always end up with an ExpressionSet containing probe sets, not genes.
> > > > 
> > > > What is an easy way to summarize/merge probe sets to (entrez) genes?
> > > > 
> > > > 
> > > > library(affydata)
> > > > library(affy)
> > > > 
> > > > # get the 'Dilution' affy batch
> > > > data(Dilution)
> > > > 
> > > > eset<- expresso(Dilution, bgcorrect.method='rma',
> > > > normalize.method='constant',
> > > > pmcorrect.method='pmonly',
> > > > summary.method='avgdiff')
> > > > 
> > > > 
> > > > write.exprs(eset,'testfile.txt')
> > > > 
> > > > 
> > > > P.S.: I know it might not be the best idea to average probe sets, but I would like to try ;)
> > > > 
> > > > Cheers
> > > > Martin
> > > > 
> > > > _______________________________________________
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> > > 
> > > 
> > > 
> > > 
> > > -- 
> > > James W. MacDonald, M.S.
> > > Biostatistician
> > > University of Washington
> > > Environmental and Occupational Health Sciences
> > > 4225 Roosevelt Way NE, # 100
> > > Seattle WA 98105-6099
> > 
> 
> 
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099