Dear Sally, You are rather expected to try reading the help pages and documentation before asking for help on this mailing list, and you don't seem to have done this. Brief descriptions of all the components produced by lmFit() and eBayes() are given in the help page help("MArrayLM-class") A more mathematical and technical description of the components in given in Sections 10.1 and 10.2 of the Limma User's Guide. Best wishes Gordon > Date: Tue, 3 Feb 2009 13:01:36 -0800 > From: "Sally" <sagoldes at="" shaw.ca=""> > Subject: [BioC] Limma and post statistical filtering of genes > To: <bioconductor at="" stat.math.ethz.ch=""> > Cc: Sally <sagoldes at="" shaw.ca=""> > Content-Type: text/plain > > Hello, > > I have used Limma for preprocessing and statistical analysis. I want to > filter my gene list after the statistical analysis but before the FDR is > applied. My analysis generates the table fit2. The fit2 table has the > following headers: > > Coefficients > df.residual > sigma > stdev.unscaled > A mean > S2.post > t > p.value > lods > F > F.p.value > > Can you explain what the following mean: stdev.unscaled, lods, s2.post, > Amean, coefficients and F.p.value mean? > > If I wanted to filter out genes by variance what would be the best way > to go? > > Sally