Dear All, I want to set up a non-specific filter to eliminate genes that are juts not expressed from further statistical analysis. I've previously tried a filter based on Mas5 presence/absence calls which turned out to be a disaster for the FDR (as measured by lots of qPCRs), probably because 1/3 of the MM probes actually hybridize better than PM, who knows. In any case, my plan is to set up a filter based both on raw fluorescent intensity and IQR. I am trying to get as much sensitivity as possible without increasing my FDR too much. I was thinking that using the intensity distributions and box plots of the raw data may be useful to determine what the best cutoffs to obtain the best sensitivity will be. Any advise on how to select appropriate cutoffs? Thank you very much in advance Lucia [[alternative HTML version deleted]]