[BioC] question on decideTests function in limma

[CHUNFA C JIE]

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