Dear Philipp, Thanks for the bug report. Now fixed in limma 2.14.2. If you wait a day, you should be able to re-install limma from Bioconductor to get the fix. The bug was unfortunately introduced when I tried to "streamline" the plotMA() code in limma 2.13.6. > Date: Tue, 20 May 2008 23:07:27 +0200 > From: Philipp Pagel <p.pagel at="" wzw.tum.de=""> > Subject: [BioC] limma: plotMA for RGList objects > To: bioconductor at stat.math.ethz.ch > > 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 Setting array=1 here is necessary because MA has only one column. Best wishes Gordon > 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