Fellow Expressionists, Does Limma automatically perform a multiple comparison adjustment for non-orthogonal contrasts? If not, can you recommend another program that can be used in conjunction with Limma to do this? Also, I find the Bayesian theory in the paper by Gordon Smyth ("Linear Models and Empirical Bayes Methods..." tough going) Can anyone please recommend a book or books on Bayesian methods that can bridge the gap between basic statistics texts (e.g. Hoel, "An Introduction to Mathematical Statistics" and Zar "Biostatistical Analysis" and this article)? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, Francis Crick