[BioC] Affy: probeset to gene expression with expresso

[Martin Preusse]

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