[BioC] Help with raw p-value
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:
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]
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"
although the t stat is same. Can someone let me know why? Thank you in
Gene Array Core Lab