[BioC] GOStat and multiple testing
sdavis2 at mail.nih.gov
Wed Aug 4 14:04:03 CEST 2004
On Aug 4, 2004, at 7:06 AM, <Arne.Muller at aventis.com> wrote:
> I was wondering if one needs to correct the p-values from the
> hypergeometirx test from GOstat for mutliple testing, since one
> performs many tests (over all GO categories found in the gene list).
> I'm not sure if correction for multiple testing makse sense since the
> GO terms are highly dependent (terms on the same branch + one gene is
> annotated in several terms).
> Robert Gentleman mentiones in the GOstats documentation that the
> multiple testing issue is not solved yet? I assume GOHyperG does not
> perform any kind of multiple testing correction, is this right?
It doesn't. I use these results as rough guides to the data, but not
something of "statistical significance". In other words, I think of it
as a means to understand the data rather than to prove something about
it. Also, making Rgraphviz plots of "significant" categories based on
some arbitrary cutoff can give you a sense of the "clustering" of your
findings in the GO DAG. This is a visual way of taking into account
the highly dependent nature of the GO.
> I'd be happy to receive comments on this and to heare about your
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