> Date: Mon, 08 May 2006 17:17:50 -0400 > From: CHUNFA C JIE <cjie1 at="" jhmi.edu=""> > Subject: [BioC] question on decideTests function in limma > To: bioconductor at stat.math.ethz.ch > Message-ID: <27808c9c2329e.445f7d3e at jhmimail.jhmi.edu> > Content-Type: text/plain; charset=us-ascii > > 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 Dear Charles, The phrase you quote refered to the B-statistics, not to the moderated-t and its p-value. Best wishes Gordon