Hi, mas5calls function is very usefull for getting p-values and P/M/A calls. I have been wondering about the discrepancy between p-value of R-affy and that of original MAS5. Today I found the reason. R-affy performs Wilcoxon test on (PM-MM) vs tau (default 0.015), on the other hand, MAS5 performs Wilcoxon test on (PM-MM)/(PM+MM) vs tau value. In my case, for example, p-values of AB000115_at were 0.018281 and 0.046482, respectively, and Detection Calls resulted in "P" and "M". Is this bug, or not? _______________________________________ Takatoshi Kawai, Ph.D. Senior Sientist, Bioinformatics Laboratoy of Seeds Finding Technology Eisai Co., Ltd. 5-1-3 Tokodai, Tsukuba-shi, Ibaraki 300-2635, Japan TEL: +81-29-847-7192 FAX: +81-29-847-7614 e-mail: t-kawai@hhc.eisai.co.jp