[BioC] Normalizing two different platforms

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Fri Feb 29 00:13:51 CET 2008

There are many posts dealing with this exact problem for these exact  
chips (for this exact reason I guess). Search the archives.


On Feb 26, 2008, at 12:07 PM, Yair Benita wrote:

> Dear R members,
> I have this problem with 2 different Affy platforms. We started the
> experiment with U133A chips but had to switch in the middle to  
> U133A_plus2.
> All the U133A are backordered with no delivery in sight. The two  
> chips have
> the exact same gene probes and differ only in a few control probes.
> Naturally I will get an error in gcrma or ReadAffy but I was  
> wondering if
> there is an easy way around this that will allow me to still  
> normalize all
> my arrays together. Can I just ignore the control probes somehow?  
> Maybe I
> need to modify the CDF file but I am not sure how complicated this is.
> Thanks,
> Yair
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