[BioC] Combining HGU133A & HGU133B data

Laurent Gautier laurent at cbs.dtu.dk
Mon Sep 15 14:48:55 MEST 2003

On Mon, Sep 15, 2003 at 06:26:15PM +0800, Adaikalavan RAMASAMY wrote:
> Dear all,
> I have been asked to analyze the data where samples were hybridized on
> both HGU133A and HGU133B Affymetrix chips. One option is to analyze the
> A and B chips seperately but this is not desirable.
> The other option is to combine both (using something akin to "rbind") to
> combine these data. I think it is better to combine the results after
> rma as different background correction needs be applied. 
> This method however does have its problems with the genes redundant
> between A and B chip (there are 2000+ genes that overlap both chips).
> Can anyone suggest what is the best way to deal with this problem ? Does
> anyone have any experience or seen publications combining data from two
> different array formats.
> Thank you.
> --
> Adaikalavan Ramasamy                      ramasamyA at gis.a-star.edu.sg
> Research Assistant
> http://giscompute.gis.a-star.edu.sg/~adai 
> Microarray & Expression Genomics          Tel: 65-6478 8043
> Information & Mathematical Sciences       Fax: 65 6478 9058
> Genome Institute of Singapore             http://www.gis.a-star.edu.sg/
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Wolgang Huber and Robert Gentleman have certainly a word to say about
that. Did you check the function 'combine' in the package 'matchprobes'
(section 'devel') ?


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