Dear All, For a data set I am working on, besides ordering coefficients by "differential expression", we are interested in getting a quick idea of whether the variance of some genes is unexpectedly large. I thought about applying the expression in p.10 of the tech. report version of Smyth's "Linear Models and Empirical Bayes Methods (...)" (http://www.statsci.org/smyth/pubs/ebayes.pdf), where s^2 ~ s_0^2 F_{d,d0} For each gene, we can compare the error variance from the linear model with the corresponding distribution from the above expression. (in R, if lmFit in fit and ebayes in fit.eb: p.vars <- pf(fit.eb$s2.post/fit.eb$s2.prior, fit$df.residual, fit.eb$df.prior) ) Does this make sense? R. -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz PGP KeyID: 0xE89B3462 (http://bioinfo.cnio.es/~rdiaz/0xE89B3462.asc)