[BioC] limma: plotMA for RGList objects

[Gordon K Smyth]

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