Hello all, I currently use SCAN to normalize Affimetrix HGU133A2 arrays, and COMBAT for treatment of batch effect in normalized arrays. I would like to implement the new UPC option - I have questions regarding : 1. From which probability is it safe to assume that feature represents true signal ? Should I cut off at 0.5, or can I only use features marked as 1? Furthermore, should all features with a low probability of being true signal be filtered out of downstream analysis, and should this filter be applied before or after using COMBAT for batch effect correction ? 2. The expression value that is the output of SCAN - these are normalized log2 values? Thank you in advance! Gadi Miron gadi.miron at gmail.com -- output of sessionInfo(): normalized1 = UPC(celFilePath, "output_file1.txt") -- Sent via the guest posting facility at bioconductor.org.