>Date: Tue, 12 Jul 2005 16:52:34 +0200 >From: "Groot, Philip de" <philip.degroot at="" wur.nl=""> >Subject: [BioC] Limma: how to calculate ordinary p-values omitting the > eBayes() command >To: <bioconductor at="" stat.math.ethz.ch=""> > >Hello all, > >Gordon Smith helpen me a while ago with calculating regularised p-values >(paired t-test) using Limma. Smyth! >Now I want to investigate the effect of the regularisation, so I also >want to calculate the ordinary p-values. The Limma User's Guide explains in a couple of places how to obtain ordinary t-statistics, for example on page 38. > tstat.ord <- fit$coef / fit$stdev.unscaled / fit$sigma > pvalue.ord <- 2 * pt( abs(tstat.ord), df=fit$df.residual, lower.tail=FALSE) > pvalue.ord.adj <- p.adjust(p.value.ord, method="fdr") Why do you want to investigate the effect of regularisation? If you don't understand the statistical procedures very well, it isn't a good idea to second-guess the methods. It is better to choose a well-respected method and stick to it. I'm not saying that you're doing this, but I suspect there is a tendency for some people to try lots of ad hoc alternatives until they get a set of p-values which suits their pet hypothesis, and this is very bad science! Gordon >Regards, >Philip