[BioC] Normalizing two different platforms

[Yair Benita]

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