Dear List, I have question about using weights, avereps and lmFit in limma. I've set weights for each spot using Flags from GenePix files. Then I normalized data and removed control spots. Next I want to replace row IDs (probe IDs) with genes IDs -- sometimes more than one probe corresponds to the same gene i.e. MZ0001 = GRMZ0001 MZ0004 = GRMZ0001 so I used avereps function to average data for rows for the same genes. The problem is that avereps averages also weights -- if MZ0001 has "0" weight and MZ0004 "1" weight, gene GRMZ0001 has weight "0.5" so it is used in lmFit, eBayes and so on. It is not desirable as one of the spots are unreliable (Bad in GenePix = weight "0"). I have an idea not to use spots with weight 0 when I compute averages. So, using above example, GRMZ0001 will have the same value as MZ0004 (which has 1 weight). Unfortunately my skills are not so high to allow me do it. Could anyone give me any hint how can I do it? Best wishes, Maciej Jo?czyk -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com