[BioC] GO over representation analysis

Joern Toedling toedling at ebi.ac.uk
Mon Aug 25 13:12:29 CEST 2008

I was quite happy with the package topGO, which allows you to supply the 
mapping between gene-identifiers and GO term IDs as a list. Such a list 
can be easily created using the biomaRt package to query the Ensembl 
database, or the list can be created from other annotation sources.
The topGO vignette and some previous posts in the archive of the 
Bioconductor list, such as the one below, may provide additional clues 
about how to perform this analysis with topGO.


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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