[BioC] limma: plotMA for RGList objects

Philipp Pagel p.pagel at wzw.tum.de
Tue May 20 23:07:27 CEST 2008

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

  MA <- MA.RG(MA[, array])
  array <- 1

in limma 2.12.0 (2007/09/25)

  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


Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
Institut für Bioinformatik und Systembiologie / MIPS
Helmholtz Zentrum München -
Deutsches Forschungszentrum für Gesundheit und Umwelt
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany

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