[BioC] Affy: probeset to gene expression with expresso

[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