If B = 1, it should return the t-value and p-value of unpermuted data, which means the result is equal to t.test for one row. I found mt.sample.teststat returns the right t-value, but mt.sample.rawp does not. Please see the following. permt<-mt.sample.teststat(golub[50,],golub.cl,B=1) >permt = 3.200749 permp<-mt.sample.rawp(golub[50,],golub.cl,B=1) >permp = 1 Furthermore, I could not understand the following histgram figure when running the example code from help >permp<-mt.sample.rawp(golub[1,],golub.cl,B=1000) >hist(permp) BTW, since mt.teststat(multtest) only return the t-value, could anybody tell me a function to get the rawp-value from a microarray data frame but Not a Permutation unadjusted p-values like in mt.maxT? Thanks --------------------------------------- > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: multtest survival Biobase "1.14.0" "2.30" "1.12.2"