On Thu, 2013-08-22 at 14:53 +0200, cstrato wrote:

> Dear Brian,
> 
> As I have already mentioned in the former case, package xps is able to 
> handle this amount of arrays.
> (Quite some time ago a user did use xps to process about 23,000 
> hgu133plus2 arrays on his Mac, and memory consumption was only 4 GB RAM.)
> 
> Best regards,
> Christian
> 

Thanks Christian,

I did take a look at xps; it seems to be something that will certainly
improve large scale analyses in R. In fact I may recommend investigating
the ROOT interface to one of my personal friends who works in health
informatics with large-scale (terabyte-sized, not petabyte) data. I
think that was the one place SAS could still beat R, but that may be
ending!

In my case, I see a number of ways to accomplish the analysis, and did
so with fRMA, but read.affybatch() seems to be failing when it could
succeed.

Thanks again,
Brian
-- 
Brian D. Peyser PhD
Special Assistant to the Associate Director
Office of the Associate Director
Developmental Therapeutics Program
Division of Cancer Treatment and Diagnosis
National Cancer Institute
National Institutes of Health
301-524-5587 (mobile)

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