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

Hi, The p-values in rawp0 are calculated based on a standard normal distribution, while those in t.test are calculated based on a t-distribution with df = 11.049. Try 2*(1-pt(abs(teststat[1]),df=11.049)) and you will get the same p-value as with t.test. Sandrine ---------------------------------------------------------------------- --------- Sandrine Dudoit, Ph.D. E-mail: sandrine@stat.berkeley.edu Assistant Professor Tel: (510) 643-1108 Division of Biostatistics Fax: (510) 643-5163 School of Public Health http://www.stat.berkeley.edu/~sandrine University of California, Berkeley 140 Earl Warren Hall, #7360 Berkeley, CA 94720-7360 ---------------------------------------------------------------------- --------- On Wed, 16 Oct 2002 donghu@itsa.ucsf.edu wrote: > 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 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >