# [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:
>*teststat[1]
*[1] 1.759195
>*rawp0[1]
*[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
advance.
Donglei Hu
Gene Array Core Lab
Diabetes Center
UCSF