Hi, The MAS5 original documentation (http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepap er.pdf) describes how the Present/Absent calls are computed. This document emphasizes that the cutoff values (alpha1=0.04 and alpha2=0.06) for attributing a P/M/A call given a P value are suitable for probesets which have between 16 and 20 probes. The man page for mas5calls states that the bioconductor implementation in the affy package uses the same values. I have 2 questions about that: 1) What are the guidelines when the number of probes per probeset is lower (11 to 14) ? 2) Does anybody knows what is the default MAS5 behaviour when the number of probes per probeset is lower ? Thanks for your help, Eric