[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
More information about the Bioconductor
mailing list