I'm trying to use sam to analyze 9 pairs of triplicate conditions, a subset of an exprSet. It takes the subset just fine, but when I feed it the following vector as cl: > cl [1] -1 -1 -1 1 1 1 -2 -2 -2 2 2 2 -3 -3 -3 3 3 3 -4 -4 -4 4 4 4 5 5 5 6 6 6 -5 -5 -5 -6 -6 -6 -7 -7 -7 7 7 7 -8 -8 -8 8 8 8 -9 -9 -9 9 9 9 > sam.out3 <- sam(subeset, cl) Error in adjust.for.mt(data, cl, var.equal = var.equal) : There is something wrong with the class labels. If I change cl to make it 18 unrelated groups, it works, but they're not paired observations. How can I get it to take these as pairs of observations? Thanks, Anand C. Patel, MD Fellow, Pediatric Pulmonology St. Louis Children's Hospital [[alternative HTML version deleted]]