Here is a very contrived example: x.temp <- rbind(c(4,4,4,4), c(1,1,4,4), c(1,0,3,4), c(1,.99999,.99998,.99997), c(1,.99999,.99998,.99998)) classlabels <- c(0,0,1,1) t.test <- mt.teststat(x.temp, classlabel = classlabels, test= "t") rawp0 <- 2 * (1 - pnorm(abs(t.test))) mt.rawp2adjp(rawp0, "Bonderroni") Output: $adjp rawp Bonderroni [1,] 0.000000e+00 0 [2,] 0.000000e+00 0 [3,] 2.209050e-05 0 [4,] 2.699796e-03 0 [5,] 4.677735e-03 0 $index [1] 1 2 3 5 4 I am not too troubled by the results of the last two rows but the first two seem to be concerning, the method does not seem to take into account zero differences. Am I correct in this account? If so, how would one fix this. Thanks Josh Software: WinXP R 1.5.0, Latest version of Multtest