[BioC] limma and 2-array divided probe sets

Wolfgang Huber huber at ebi.ac.uk
Mon Apr 20 15:03:37 CEST 2009

Jorrit Boekel ha scritto:
> Dear list,
> I would like to do an analysis on a published dataset that used the 
> "previous generation" (quote Affy) arrays Mu11K. These contain ~11K 
> probes divided over 2 chips, give rise to 2 cel files, and use different 
> annotation packages.
> As I am no limma-veteran, I wondered if there was a way to concatenate 
> the data from these files before or after reading it into limma as two 
> separate affybatch objects, and then make an eSet. If not, should I 
> instead analyse the chips separately and merge the resulting toptables?
> cheers,

Dear Jorrit

it is better to do the normalisation and quality control separately. For 
whether you then merge pre or post differential expression analysis with 
limma, I don't see any big concerns either way, that is probably more a 
question of what you find more convenient.

Best wishes

Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber

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