Dear Users, If you use LPE package, this information may be helpful for you. Based on my experience, LPE package is very useful to identify differentially expressed genes for data sets with very small sample size. One thing that did not/not clearly document in the user manual is that when the sample size in each group is larger than 5, the results will keep changing when you run the SAME code many times. I happen to find this comes from subrountine (am.trans) called by lpe function. > am.trans function (y) { if (ncol(y) > 5) y <- y[, sample(1:ncol(y), 5)] # here makes the results keep changing n <- ncol(y) if (n < 2) { stop("There are no replicated arrays!") } A <- c() M <- c() cc <- permute(1:n) for (i in 1:(n - 1)) { A <- c(A, c((y + y[, cc[i, ]])/2), recursive = TRUE) M <- c(M, c(y - y[, cc[i, ]]), recursive = TRUE) } return(cbind(A, M)) } Therefore, when you use lpe pacakge and when one of your groups in your dataset has more than 5 samples, you shold notice that your results will be changing. You can fix this problem by commenting out the code # if (ncol(y) > 5) # y <- y[, sample(1:ncol(y), 5)] Pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital for Sick Children Research Institute MaRS Centre - East Tower 101 College Street, Room 15-705 Toronto, Ontario, M5G 1L7, Canada Tel.: (416) 813-7654 x6016 Email: phu at sickkids.ca Web: http://www.tcag.ca/statisticalAnalysis.html