[BioC] GOStat and multiple testing

[Stephen Henderson]

 Perhaps correction of multiple testing in this case is not so important as
the GO terminology itself is such a subjective entity. GOstats then can be
viewed as a useful tool and scores as a useful index, but an attempt to
attain exactness is flawed at a level prior to enumeration. To create them
may only encourage over-interpretation.


-----Original Message-----
From: Arne.Muller
To: bioconductor
Sent: 8/4/04 12:06 PM
Subject: [BioC] GOStat and multiple testing

Hello,

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?

I'd be happy to receive comments on this and to heare about your
experience.

	kind regards,

	Arne

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