Hi, With limma, the moderated-t and its p-value provide a ranking guide because the various sorts of underlying assumptions are never exactly true for microarray data. The decideTests() fucntion makes multiple testing adjstment and declares significance. My question: Dr. Smyth says the moderated-t and its p-value "are intended to be taken as a guide rather than as a strict measure of the probability of differential expression". Then how does decideTests() fuction declare significance (yielding -1, 0, 1)? Are the underlying assumptions assumed when using decideTests()? Chunfa (Charles) Jie, Ph.D./ M.S. JHMI Microarray Core School of Medicine Johns Hopkins University BRB 355, 733 W Broadway Baltimore, MD 21205 Phone: (410) 502-6659 Fax: (410)502-7543 Email: cjie1 at jhmi.edu