[BioC] Memory issue on Linux running Affymetrix HG-U133_Plus_2

James W. MacDonald jmacdon at med.umich.edu
Thu Jan 19 20:26:56 CET 2006

Dmitry wrote:
> Hi all,
> I've read here that nobody had a problem running gcRMA on Linux.
> Surprisingly I do.
> I run 36 HG-U133_Plus_2 cel files using 1G of RAM and 2G of swapping memory
> and get this message
> Error: cannot allocate vector of size 359894 Kb
> Note that regular RMA runs just fine.
> Then I read specifications for gcRMA and found recommendation to have 1.25G
> of RAM.
> So I've upgraded my machine to 1.5G and got exactly the same message
> Error: cannot allocate vector of size 359894 Kb.
> What else could you recommend to solve the problem?

justGCRMA() is designed to solve this problem.



> Is it feasible to split gcRMA runs then combine data in Excel and normalize
> it using column average?
> Thank you
> Dmitry
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James W. MacDonald
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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