[BioC] Affy: probeset to gene expression with expresso

[Martin Preusse]

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
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> Seattle WA 98105-6099