Dear YSong, Try something like this: # you need to specify the probesets that you want accession numbers for in the first argument to mget library(mouse4302.db) mapping.pid.acc <-unlist(mget(c("1415673_at","1415675_at"), mouse4302ACCNUM)) #>mapping.pid.acc #1415673_at 1415675_at #"NM_133900" "BC008256" #i.e this will return all the probeid accession numbers mapping.pid.acc <-unlist(mget(featureNames(rma.data), mouse4302ACCNUM)) Regards, Amos Folarin ------------------------------ Message: 4 Date: Mon, 2 Aug 2010 09:18:57 +0800 From: Yisong Zhen <zhenyisong@gmail.com> To: bioconductor at stat.math.ethz.ch Subject: [BioC] probe ID<-> accession number Message-ID: <aanlkti=f6rdnzqqvu0vnhtsubq_n6vcw1hbq1+k92uyr at="" mail.gmail.com=""> Content-Type: text/plain Dear All, I use the following code to generate HTML report on deferential expression genes after LIMMA analysis. The code is from Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Now, I want to add a column in the final output, which includes the gene accession number of reference sequence, for example, NM_008725 besides gene entrez ID and gene name. In this way, I could match probe ID to their corresponding accession number. But how can I write a code to implement it? Thanks in advance. YiSong PS. library("annotate"); library("mouse4302.db"); totalGeneNumber<-dim(exprs(rma.data))[1]; iso_control<-topTable(fit2,coef=1,adjust.method="BH",number=totalGeneN um ber); genenames = as.character(iso_control$ID); sym<-getSYMBOL(genenames,"mouse4302"); ll<-getEG(genenames,"mouse4302"); iso_control=data.frame(sym,signif(iso_control[,-1],3)); htmlpage(list(ll),othernames=iso_control,filename="iso_control.html",t it le="HTML report", table.center=TRUE, table.head=c("ENTREZ ID", colnames(iso_control))); [[alternative HTML version deleted]] ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 90, Issue 1 ******************************************* ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (it.support at cancer.ucl.ac.uk). **********************************************************************