[BioC] GOStat and multiple testing

[Sean Davis]

On Aug 4, 2004, at 7:06 AM, <Arne.Muller at aventis.com> wrote:

> 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?

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 
> experience.