Hi, I'm using Limma to find differentially expressed genes in a set of 2 replicate two-colour arrays, and I would like to know precisely how lmFit takes into account the weights I gave to the spots. My question arises because in the topTable of differentially expressed genes, I see genes for which one spot had been flagged out as bad on one array, but not on the other. Those genes don't appear in the top 100, so it's not a huge deal, but I was surprised those genes showed up at all. Does lmFit give some kind of penalty during the fitting to genes for which we have fewer data points than the total number of arrays, because they have been flagged out on some of the arrays? Cheers, Jeremy