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

Sean Davis sdavis2 at mail.nih.gov
Mon Dec 18 20:17:06 CET 2006

On Monday 18 December 2006 14:05, 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.

I haven't tried it, but justGCRMA and justRMA are designed to be 
memory-efficient.  Have you tried either of those?

> Anybody knows how GNF was processed and normalized? (158 arrays)

They are available here (http://wombat.gnf.org/index.html) as either gcRMA or 
MAS5 normalized.  Also, the raw data are available from them as .CEL files.  
You can contact them and they will even send you a DVD, if I recall.


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