[BioC] biomaRt and rma

[James W. MacDonald]

Hi Naomi,

On 3/12/2014 4:20 PM, Naomi Altman wrote:
> 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?

You can also use the annotation package for this array, rat2302.db:

library(rat2302.db)
gnids <- select(rat2302.db, features, "ENTREZID")

Best,

Jim
>
> Thanks for any insights.
>
> --Naomi
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099