[BioC] biomaRt and rma

Naomi Altman naomi at stat.psu.edu
Wed Mar 12 21:20:29 CET 2014


I have been trying to use biomaRt to get entrezIDs for my Affymetrix 
probesets.

This works fine, but is not what I want:

library(affy)
CELdata=ReadAffy(celfile.path=celfileDir)
features=featureNames(CELdata)

library(biomaRt)
ensembl = useMart("ensembl",dataset="rnorvegicus_gene_ensembl")
getBM(attributes=c('affy_rat230_2','entrezgene'), filters 
='affy_rat230_2', values = features[1:20], mart = ensembl)

What I want is the entrezIDs for the probesets, as compiled by rma:

data.rma=rma(CELdata)
features=featureNames(data.rma)

Are these affyIDs not available in biomart?  Am I using the wrong filters?

Thanks for any insights.

--Naomi



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