[BioC] Combining HGU133A & HGU133B data

[Crispin Miller]

Hi,
A more serious issue is that normalisation (almost certainly) assumes that the average expression level on each chip is the same. This is clearly not the case between A and B chips - and combing each pair of A's and B's for every sample, before normalisation, is almost certainly a bad idea... 

Normalising the A's and B's separately is probably much more sensible - and this then allows you to use the 2000+ shared probes to see how well your normalisation has worked: their signals are from the same hyb. cocktail so they should produce the same expression levels. If you think about it this way, the repeated probes are a Good Thing(TM) :-)

Crispin


> -----Original Message-----
> From: Adaikalavan RAMASAMY [mailto:ramasamya at gis.a-star.edu.sg]
> Sent: 15 September 2003 11:26
> To: bioconductor at stat.math.ethz.ch
> Cc: Mark.Reimers at biosci.ki.se
> Subject: [BioC] Combining HGU133A & HGU133B data
> 
> 
> 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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