[BioC] combining p-values for multiple genes using stouffer
sdavis2 at mail.nih.gov
Tue Apr 15 11:34:52 CEST 2008
On Tue, Apr 15, 2008 at 1:01 AM, william ritchie <billthebrute at yahoo.fr> wrote:
> Dear Bioc community,
> I have a little question about combining p-values with stouffers method.
> One of the conditions for combining p-values is that each test be considered as independent.
> If I was interested in a group of say, 10 genes and I wanted to know if, as a group, they were significantly over or under expressed, would it be correct to combine the p-values (calculated from a series of microarrays) for each individual gene using stouffers method to be able to conclude that this group of genes is differentially expressed ?
Hi, William. Assuming independence among genes is problematic. Why
not use one of the many Gene Set Enrichment approaches (PGSEA, limma
gene set test, globaltest, to name just a few). Alternatively, you
could use permutation to get a level of significance for your
Stouffer's p-value, but I think it might be problematic to take the
Stouffer's p-value directly as the measure of significance.
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