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

It seems like a given that as soon as I send a message to the list, the problem corrects itself. --Naomi

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099