[BioC] Memory problems with RMA

[Moore, Stephen]

Dear List,

I have downloaded 100 samples of Affymetrix U133 Plus 2.0 array (more than 50,000 probes) from the web. We read those files into R by using ReadAffy( ) and tried carrying out the normalization by using rma( ). However we have encountered the problem of short of memory. I use Windows 2000 on PC and the memory is 1 GB. Is there some code in R for reading the CEL files one by one and some code to read the data row by row for rma, which may help our available memory deal with 'read files into R' and 'rma' commands.  Has anyone met this problem with this size of dataset before and if so what can we do to correct the situation (possibly by running R on a unix server?).

Dr. Stephen Moore
Senior Scientist
ArraGen Ltd.
Almac House
Seagoe Industrial Estate
Craigavon
Co. Armagh
BT63 5QD
Northern Ireland
E-mail:Stephen.Moore at arragen.com
Phone: 02838 395751
Mobile: 07719 989348
Fax:     02838 398676