Dear Colleagues I have a question about how the AveExpr value gets calculated in limma topTable. Actually, it appears to get calculated in lmFit, e.g., from lmFit: $Amean uc007aet.1 uc007aeu.1 uc007aev.1 uc007aew.1 uc007aex.1 0.8269211 1.1462191 -2.3369824 -6.0639390 -8.4696942 from topTable: acomps.txt:uc007aet.1 -1.07454088439694 0.826921104052945 -0.83217169279942 0.413619779606768 0.999993313025155 -5.09985857376248 bcomps.txt:uc007aet.1 -0.590082310688743 0.826921104052945 -0.559690866321207 0.580942531774888 0.999999437256152 -4.75598562188099 So AveExpr = Amean But I have looked at the 'average log-intensity' for the raw values and for the fitted coefficients for log10, log2 and log and looked at mean(log(x)) and log(mean(x)) and I can't get 0.8269211. I can post the data if need be. Moreover, many of the fitted coefficients are less than zero and log(mean(x)) is defined but not mean(log(x)). Can anyone tell me how Amean (and therefore AveExpr) gets calculated? Thanks Mike Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806