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

[James W. MacDonald]

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.

HTH,

Jim


> 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
734-647-5623