[BioC] GOstats suggestion

Joern Toedling toedling at ebi.ac.uk
Mon Jun 4 15:50:25 CEST 2007

Hello Johannes,

you can use BioConductor's "AnnBuilder" package to produce a custom
annotation package for your own selection of EntrezGeneIDs and then use
GOstats with this custom annotation package. This may be more efficient
than mapping EntrezGeneIDs to GO nodes each time you run GOstats. Having
said that, I have to admit that it took some time to get AnnBuilder
running due to its dependencies.

Best regards,

Johannes Rainer wrote:
> dear Seth, dear Bioconductor members,
> as far as i understand you are using the annotation package defined with the
> "annotation" parameter (GOHyperGParams) to map the submitted EntrezGeneIDs
> to the GO terms. this works fine for Affymetrix arrays with available
> annotation packages, but we are for example also using Exon arrays and are
> annotating the probes on our own. my suggestion is to support also the
> mapping from EntrezGene IDs to GO terms using the GO package. this would
> allow GO analyses for all microarray platforms, not just Affmetrix arrays
> with available annotation packages.
> sincerely, jo

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