> Gordon, > > Just a quick question using Limma. I want to form a table with p-value > in columns and genes in rows for multiple contrasts and for all genes. It seems to me that the eBayes() function does exactly this. > Ultimately, I want to be able to determine the genes that have p<alpha> for some proportion of the experiments (2/3, for example). I don't believe in this sort of analysis. One combined p-value seems better. But the p.value component returned by eBayes() makes it easy if you want to do it. Gordon > A more involved question that you needn't answer if you don't have time, > but could I use classifyTests to do the same thing (find all genes that > are "significant" over a set of experiments)? > > Thanks, > Sean