[BioC] Combine dataset from different chip

[Marc Carlson]

Tom wrote:
> Some additional information:
>
> My data comes from two different type of microarray: hgu133a and hthgu133a
> I want pre-process my data to obtain only one ExpressionSet that contain the
> merged data.
>
> What I want to do is:
> - merge the two batches with combineAffyBatch function 
> - normalize the data (for example with rma)
>
> Is this a good way to pre-process my data?
>
> Any suggest is appreciated. 
> Thanks in advance.
>
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>   
My advice is that you will want to be very careful here because there
are strong batch effects for the different chip types.  That is, a given
probeset "X" will behave very differently on one chip type than on
another.  I would try to avoid doing this if possible, but if you
cannot, then you will probably have to find a statistician to help you
try to adjust between these two different groups.  Hopefully you will
have all the things you want to compare represented well on both
platforms?  Otherwise your going to find yourself hip-deep in false
positives.

    Marc