[BioC] GO-Analysis using TopGO for Yeast2 data

Marc Carlson mcarlson at fhcrc.org
Tue Mar 25 17:04:03 CET 2008

Tobias Koschubs wrote:
> Hi!
> I tried to do a GO-Analysis using the TopGO package with Affymetrix 
> Yeast2 Expression data but encountered a couple of problems. As I'm new 
> to Bioconductor, I would be very grateful to get some help.
> The Yeast2-Package related problems are the following: Very recently, 
> the GO-Annotations have been updated and now include also the 
> annotations from computationally predicted methods (available from 
> yeastgenome.org and geneontology.org). Of course, I would like to use 
> the newest annotations and I tried to use the AnnBuilder 
> yeastPkgBuilder-method. However, I didn't succeed to bring the 
> gene_association.sgd file together with the Probe mappings on the chip. 
> I guess one would need to use the ORFs as identifiers instead of the 
> SGD-identifiers from the gene_association file. Moreover, I didn't 
> figure out how to set the path for the annotation file as local (it was 
> suggested to unpack it in advance). Is there someone from the Biocore 
> Data Team who has the proper scripts to do it?
> With the TopGO package, I did the GO Analysis using the current yeast2 
> annotations. Unfortunately, it's documentation lacks some details and I 
> didn't figure out, how to print out the genes (or at least the probes) 
> according to the top-GO-terms listed by the genTable-Method. From the 
> source-code, I learned that there's a printGenes-method which possible 
> should do this. However, the yeast2 chip is a bit different from others 
> as it doesn't use ENTREZIDs or SYMBOLS and I also didn't figure out what 
> are the parameters of this method.
> Best and thanks in advance,
> Tobias Koschubs
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It's hard to help you because we don't have the results of your
sessionInfo() or the code you were trying to run.  You might want to
look here for some helpful tips on how to ask questions of the boards:


So presently, I am just not sure if this is what you need or not, but I
will make a guess and tell you that if you want to get the usual gene
symbols from the yeast2 package, you should be looking at the
yeast2GENENAME map.


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