[BioC] Affy: probeset to gene expression with expresso
Martin Preusse
martin.preusse at gmail.com
Tue Aug 13 15:47:28 CEST 2013
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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