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From: AC on 7 Jul 2010 06:59
Hi,

I have 2 questions about geneontologydemo.m :

1. I am having a hard time understanding how the p-values are computed. In the demo:

pvalues=hygepdf(upgenesCount,max(chipgenesCount),...
max(upgenesCount),chipgenesCount);

This is weird to me. Shouldn't it be:

pvalues=1-hygecdf(X,M,K,N);

with
X=upgenesCount;
M=total number of genes;
K=number of genes in GO term;
N=number of upgenes
?

Why is it so different? How is the first one correct?

2. Should we be correcting for multiple testing? (e.g Benjamini-Hochberg proc)

Could someone shed some light?

Thanks a lot!
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