Hi, Hamid.  Your best bet in the future to reach the largest audience is to
write to the bioconductor user list and not bioc-devel.

To answer your question, you might try aroma.affymetrix or the xps package.
I think these will handle your 400 arrays pretty well and you will not need
to split up the groups.

Sean


On Wed, Feb 18, 2009 at 1:47 PM, Hamid Ashrafi <ashrafi_h@yahoo.com> wrote:

> Hi All,
>
> I have got ~400 CEL files that need to be normalized together. Affy batch
> can handle upto ~200 CEL files, if you have 400 you will get an error
> message right the beginning before even be worry about your memory capacity.
> Recently AffyPara has introduced that enables you to run a large batch on
> clusters. However, if I continue to normalized them in two 200 batches on a
> single machine. How different the results would be compare to normalizing
> all 400 together. These CEL files are from a RIL population the should
> pretty much homogeneous.
>
> Thanks,
>
> Hamid
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