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

Yair Benita yair.benita at gmail.com
Mon Dec 18 20:05:21 CET 2006

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.

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,

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