[BioC] GOStat and multiple testing

[Robert Gentleman]

On Wed, Aug 04, 2004 at 01:06:30PM +0200, 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?

Hi,
  it does not, and I am unaware of any general solution to the
  problem of adjusting p-values here. The structure of GO is such that
  there are issues due to lack of independence. There are some other
  problems, but I have not had time to write up my ideas yet.
  I have to say that I am also not so convinced that this is
  the best way to do things (classifying genes as interesting or not,
  and then doing the hypergeometric test), although I have yet to come
  up with a better way. I agree with those that have suggested that
  this is best used as a rough guide to interesting categories (others
  projects seem have different opinions, and I think some do use some
  sort of p-value correction). 

  Robert

> 
> I'd be happy to receive comments on this and to heare about your experience.
> 
> 	kind regards,
> 
> 	Arne
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
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