[BioC] Help for GOstats packages

[Carlson, Marc R]

Hi Fabrice,

You have a couple of different options you could consider.  You can either use the SQLForge code from the AnnotationDbi package to try and generate a custom .db package, OR you can just follow the instructions in the GOstats package called "Hypergeometric tests for less common model organisms".  You can find these instructions here: 

http://www.bioconductor.org/help/bioc-views/release/bioc/html/AnnotationDbi.html

or here:

http://www.bioconductor.org/help/bioc-views/release/bioc/html/GOstats.html


  Marc



----- Original Message -----
From: "Fabrice Tourre" <fabrice.ciup at gmail.com>
To: rgentlem at fhcrc.org, "Bioconductor mailing list" <bioconductor at stat.math.ethz.ch>
Sent: Wednesday, February 16, 2011 3:27:41 PM
Subject: [BioC] Help for GOstats packages

Hi list,
I want to use GOstats packages to do Gene Ontology analysis. My chip
array is Affymetrix Human Exon 1.0 ST. But it seems that I can not
find annotation data for this array on
http://www.bioconductor.org/help/bioc-views/release/data/annotation/
Does anyone has some suggestion that I can use GOstats to do GO
analysis with my array?
Thanks.

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