[BioC] Sweave & limma mystery

[Philipp Pagel]

On Tue, Jun 03, 2008 at 06:38:41AM +0200, Matthias Kohl wrote:
> to generate your plot on different devices, the code in your document  
> has to be executed more than once. Hence, the modification of your  
> object MA works as expected in the first run, but also has an influence  
> on further runs. This is not a specific problem which occurs only with  
> plotMA.

Thanks for the reply! Of course you are right - I hadn't thought about
that. 

> I would recommend to introduce
>
> MA0 <- MA
> MA0$weights[MA0$genes$Status != 'gene', ] <- 0.0

That's how I had worked arout it - but didn't quite grasp what the
reason was.

So the only question remaining is: Why on earth does Sweave generate all
plots on both devices? But I guess I should o to r-help with that
question - or maybe I should scrutinize the Sweave manual yet another
time...

Thanks
	Philipp

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