[BioC] about: p.value, adj.p.val, F.p.value

yanju yanju at liacs.nl
Mon Nov 27 17:47:41 CET 2006


Dear all,

I am just a little bit confused about p.value, adj.p.value and 
F.p.value. Could somebody tell me what are the proper cases to use them? 
I am supposed to detect the differenct expressed genes with the p-value 
less than 0.05, therefore, my code is like follows:
    fit<-eBayes(fit)
    selected<-p.value<0.05

But in Limma user guide, the code is like this:
    selected<-p.adjust(fit$F.p.value, method="BH") <0.05
here the F.p.value is used.

And also if i choose the top10 different expressed genes like this:
    topTable(fit, adjust="BH")
there is a adj.p.value.

So I really want to know when to use which. Expecting your reply.

Regards,
Yanju



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