[BioC] geneSetTest() / GESA

Simon Lin simonlin at duke.edu
Sun Mar 4 19:46:19 CET 2007


Dear Gordon,

Is the geneSetTest() fast to calculate? Not sure if you used permutation 
test under the hood.

For GSEA and GSA, sometimes we see artifacts when the size of the set is too 
small. Is the same true for geneSetTest?

Thanks!

Simon


Date: Sun, 04 Mar 2007 18:51:00 +1100
From: Gordon Smyth <smyth at wehi.EDU.AU>
Subject: [BioC]  GSEA with one class metaanalysis
To: Mark W Kimpel <mwkimpel at gmail.com>
Cc: bioconductor at stat.math.ethz.ch
Message-ID: <6.2.5.6.1.20070304184303.0242d7a0 at wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed

Dear Mark,

If I understand your problem correctly, neither GSEA nor GSA will
accomodate it. The only option I know of is geneSetTest() in the
limma package. This generally works well, although it will give you
someone over optimistic p-values if there are strong positive
correlations between the genes in your gene sets.

Best wishes
Gordon



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