No, there is no way to get individual p-values corresponding to the nestedF method. You can however just used the overall F-test p-values, fit$F.p.value, which will give you p-values at the probe level rather than the contrast level. Use p.adjust(fit$F.p.value) to get adjusted p-values. The nestedF method will give at least one significant contrast for a given probe if and only if the above adjusted p-value is less than the cutoff. Best wishes Gordon > Date: Thu, 16 Feb 2006 17:17:08 +0100 > From: Georg Otto <georg.otto at="" tuebingen.mpg.de=""> > Subject: [BioC] Question: limma decideTests nestedF p-values > To: bioconductor at stat.math.ethz.ch > > Hi! > > I am using decideTests with the method "nestedF" to get differentially > expressed genes. My question is: how can I use nestedF (or > heirarchical) to get the actual adjusted p-values (instead of -1,0,1)? > > Best, > > Georg