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Question: probe ID<-> accession number
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gravatar for Yisong Zhen
7.3 years ago by
Yisong Zhen200
Yisong Zhen200 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? 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$ID); sym<-getSYMBOL(genenames,"mouse4302"); ll<-getEG(genenames,"mouse4302"); iso_control=data.frame(sym,signif(iso_control[,-1],3)); htmlpage(list(ll),othernames=iso_control,filename="iso_control.html",t itle="HTML report", table.center=TRUE, table.head=c("ENTREZ ID", colnames(iso_control))); [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.3 years ago by James W. MacDonald45k • written 7.3 years ago by Yisong Zhen200
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gravatar for James W. MacDonald
7.3 years ago by
United States
James W. MacDonald45k wrote:
Hi YiSong, On 8/1/10 9:18 PM, Yisong Zhen wrote: > Dear All, > > I use the following code to generate HTML report on deferential expression > genes after LIMMA analysis. The code is from Bioinformatics > and Computational Biology Solutions Using R and Bioconductor. Now, I want to > add a column in the final output, which includes the gene accession number > of reference sequence, for example, NM_008725 besides gene entrez ID and > gene name. In this way, I could match probe ID to their corresponding > accession number. > > But how can I write a code to implement it? For Affy arrays, you might consider using the annaffy package, which will output arguably nicer tables than the htmlpage() function is capable of. And for a bit of self promotion, you might look at the affycoretools package, which IMO further streamlines things. Best, Jim > Thanks in advance. > > YiSong > > > PS. > > library("annotate"); > library("mouse4302.db"); > > totalGeneNumber<-dim(exprs(rma.data))[1]; > iso_control<-topTable(fit2,coef=1,adjust.method="BH",number=totalGen eNumber); > genenames = as.character(iso_control$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
ADD COMMENTlink written 7.3 years ago by James W. MacDonald45k
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