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Question: combining p-values for multiple genes using stouffer
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gravatar for william ritchie
9.6 years ago by
william ritchie20 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 ? Thanks, william. ____________________________________________________________ ente http://mail.yahoo.fr
ADD COMMENTlink modified 9.6 years ago by Sean Davis21k • written 9.6 years ago by william ritchie20
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gravatar for Sean Davis
9.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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. Sean
ADD COMMENTlink written 9.6 years ago by Sean Davis21k
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