Hi BioC, I've had a good hunt through the documentation but can't find a solution to this. Is it possible to determine between which classes a probes has a delta value above the threshold and perhaps output that along with the significant probes? For example Say the following design cl <- c(4,9,7,8,1,7,6,4,1,2,3,4,4,7,8,2,9,3,8,6,2,2,3,9,7,8,1,4,1,2,7,2,8,5, 5, 1,9,9,3,5,3,5,5,1,9,7,8,6,6,4,6,5,3) sam.out <- sam(eset.rma, cl, rand = 123) Can I extract sat and list of 1-3,1-7 showing a probe was differential for those comparisons from the sam.out object? Many thanks Elliott This message has been scanned for viruses by BlackSpider...{{dropped:3}}