[BioC] How to read and normalize hundreds of CEL files?

James W. MacDonald jmacdon at med.umich.edu
Mon Dec 18 20:16:05 CET 2006

Hi Yair,

Yair Benita wrote:
> Dear Bioconductors,
> I am trying to read and normalize 230 microarray CEL files (Affy U133A).
> This is obviously very difficult since it requires a lot of RAM and always
> fails with an alloc error. I tested it on a dual Xeon (2.3Ghz) linux machine
> with 4Gb of RAM, but failed at the ReadAffy command.
> Except from finding a high-end machine with lots of RAM and CPU power, is
> there a way to run this on a normal computer?
> Theoretically, it should be possible to read and write to hard-drive. I
> don't mind if it takes 2 or 3 days, just as long as it will possible to do.

I know someone who just did around 1000 U133 Plus 2 chips using a Linux 
box with 16 Gb RAM using justRMA(), so I am betting you can do all 230 
with your comp. The downside of this is you won't be able to do many QC 


> Is there a way to break down ReadAffy and gcrma to smaller subsets and then
> combine them to one matrix of genes x samples?
> Anybody knows how GNF was processed and normalized? (158 arrays)
> Thanks for the help,
> Yair
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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