[BioC] GO over representation analysis

Marc Carlson mcarlson at fhcrc.org
Mon Aug 25 18:02:43 CEST 2008

You could just make an annotation package for the array in question by 
using the SQLForge code in the AnotationDbi package.
You can find instructions on how to do this here:


Let me know if you have any questions about SQLForge.


Heike Pospisil wrote:
> Hello Bioconductors,
> I am looking for a method to perfom over representation analysis (Gene 
> Ontology) within R. I have data from the Maize Oligonucleotide Array (two 
> channel) with the GO categories for all probes on this array. I have 
> clustered the genes using Maanova and I am interested in GO over 
> representation of the gene lists from these clusters.
> I know the GO tools from Bioconductor (e.g. GOstats), but I do not know how to 
> adapt the analysis to an 'unusual' array with no annotation data package and 
> now Entrez IDs. Any hints?
> Thanks in advance,
> Heike

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