[BioC] Help with raw p-value

donghu@itsa.ucsf.edu donghu@itsa.ucsf.edu
Wed, 16 Oct 2002 15:54:56 PDT

I have played with multtest package using Golub data.  After loading the
dataset, I followed the steps descripted in the document to calculate t
stat and raw p-values.  Here are what I did:

>teststat <- mt.teststat(golub, golub.cl)
>rawp0 <- 2*(1-pnorm(abs(teststat)))

Then I took a look of the t stat and raw p-value of the first gene.  I got:

[1] 1.759195
[1] 0.07854436

I also tried to calculate t stat and p-value of the first gene using
t.test.  I did the followings.

> x <- golub[1,1:27]
> y <- golub[1,28:38]
> t.test(x,y)

The result showed "t = -1.7592" and "p-value = 0.1062".  I don't
understand why the "p-value" I got here is different from "rawp0[1]"
although the t stat is same.  Can someone let me know why?  Thank you in

Donglei Hu
Gene Array Core Lab
Diabetes Center