[BioC] Combining HGU133A & HGU133B data

[Adaikalavan RAMASAMY]

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/