[BioC] handling multiple gal files in limma

Gordon K Smyth smyth at wehi.EDU.AU
Wed Mar 18 23:14:27 CET 2009

Dear Mark,

The short answer is that limma always assumes a common gal file for all 
arrays, so there are no automatic ways to handle two or more gal files.

It is sometimes necessary to handle multiple gal files, when the basic 
library of probes remains the same, but this requires special programming, 
and should be considered only when you really know what you're doing. 
For general gal files, trying to combine just doesn't make sense.

Best wishes

> Date: Wed, 18 Mar 2009 09:54:28 -0000
> From: "mark alston \(IFR\)" <mark.alston at BBSRC.AC.UK>
> Subject: [BioC] handling multiple gal files in limma
> To: <bioconductor at stat.math.ethz.ch>
> Content-Type: text/plain
> Hi,
> I'm new to the mailing list and to R/limma so please be gentle.
> I found a previous posting (Sept. 2007 - 'different gal files using
> limma') on how to deal with two gal files in limma but is it possible to
> handle > 2 gal files?
> In short, can you cbind(MA1, MA2, MA3) ?
> Regards,
> Mark
> ******************************************
> Dr Mark Alston,
> Computational Biologist,
> Institute of Food Research,
> Norwich Research Park, Colney,
> Norwich NR4 7UA, UK.
> Tel      +44 (0)1603 251432
> e-mail  mark.alston at bbsrc.ac.uk
> www.ifr.ac.uk
> www.foodandhealthnetwork.com
> www.ifr.ac.uk/edisclaimer
> ******************************************

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