> Date: Tue, 19 Jul 2005 10:37:42 +0200 > From: Matja? Hren <matjaz.hren at="" nib.si=""> > Subject: [BioC] Weights in limma package (theoretical question) > To: <bioconductor at="" stat.math.ethz.ch=""> > > To all users of limma, > > We are using limma package for differential gene expression analysis. We also use weights (0 and > 1) based on quality control from image analysis. We know that spots with weight 0 are not included > into normalisation of data (although the MA values are calculated for them also - as explained in > Limma User's Guide). Our question is what happens with these "0-weight" spots during further DE > analysis in limma package? By default, such spots will be ignored in the DE analysis conducted by lmFit() etc. > Is there any chance that they might appear in the toptable? What to do in that case (simply ignore > them)? Or do you suggest filtering them out after normalisation? Your question is not well-posed, because weights apply to *spots*, while it is *probes* which appear in topTable. There are a whole string of spots belonging to each probe, one or more for each array in the experiment, so a spot does not equal a probe. A probe can still show up near the top in topTable if some of its spots are given zero weight. On the other hand, if all the spots corresponding to a given probe are given weight zero, then that probe will get a NA p-value and will definitely not show up in topTable. This is the intended behaviour. Gordon > Matjaz and Spela > > National Institute of Biology, Ljubljana, Slovenia