With a recent update of bioconductor it appears to me that a little bug has been introduced into plotMA() in the limma package: Selecting the desired array with plotMA(foo, array=2) does not work anymore if foo is an RGList. The reason seems to be a small change in the respective part of the source code from MA <- MA.RG(MA[, array]) array <- 1 in limma 2.12.0 (2007/09/25) to array <- 1 MA <- MA.RG(MA[, array]) in limma 2.14.1 (2008/05/08). In fact, I didn't understand why array is set to 1 in the first place. Or is his really a feature and I just fail to see why this is correct behavior? cu and thanks for any enlightenment Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany and Institut f?r Bioinformatik und Systembiologie / MIPS Helmholtz Zentrum M?nchen - Deutsches Forschungszentrum f?r Gesundheit und Umwelt Ingolst?dter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel