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 umber); 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 itle="HTML report", table.center=TRUE, table.head=c("ENTREZ ID", colnames(iso_control))); [[alternative HTML version deleted]]

Hi YiSong, On 8/1/10 9:18 PM, Yisong Zhen wrote: > 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? For Affy arrays, you might consider using the annaffy package, which will output arguably nicer tables than the htmlpage() function is capable of. And for a bit of self promotion, you might look at the affycoretools package, which IMO further streamlines things. Best, Jim > 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=totalGen eNumber); > 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" ,title="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 > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues