[BioC] probe ID<-> accession number

James W. MacDonald jmacdon at med.umich.edu
Mon Aug 2 22:38:52 CEST 2010

  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.



> 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=totalGeneNumber);
> 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]]
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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