[BioC] Help using ENSMUSG ids in GOstats

Robert Gentleman rgentlem at fhcrc.org
Sun May 11 00:07:39 CEST 2008

John Reid wrote:
> Hi,
> I have some sets of genes I wish to test for enrichment against a 
> background set of genes. These genes are identified by Ensembl 
> identifiers. I have found it quite straightforward to use the topGO 
> package to do this.
> I would also like to use the GOstats package and test for enrichment 
> against KEGG pathways. It looks as if I need to create an annotation 
> package to do this. Is this straightforward? I didn't find out how to do 
> it from the documentation. My guess is that someone has been in this 

  Hi John,
    You don't give us much to work from.

I am guessing you have not looked at either AnnotationDbi or AnnBuilder 
as packages that you can use to build an annotation package.

    I am also guessing you have not searched the email list archives for 
any of the several previous discussions (that is a good place to start).

   You don't tell us what organism, but I suspect that you could simply 
use one of the organism based annotation packages (without needing to 
build anything).  There are several previous threads on how to do that.

   Best wishes

> situation before. I should say the genes come from a computational 
> analysis and not from a microarray.
> Any help appreciated,
> John.
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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