[BioC] affy & problems with memory

James W. MacDonald jmacdon at med.umich.edu
Tue Jan 10 20:01:36 CET 2006

Ettinger, Nicholas wrote:
> Hello all!
> I have 16 Affy Hg-U133plus2 cel files that I am trying to analyze.  I am
> having difficulties generating expression data because of memory
> problems.  I am working on a Dell desktop running WinXP.  I can
> successfully generate expression values if I use "RMA" but if I try MAS5
> or GCRMA or LiWong instead then I consistently get an error message with
> "Cannot allocate vector of size 169362 Kb."  To try to increase
> available memory I have already done two things:  (a) I right-clicked on
> the R icon and changed the box labeled 'Target' to read "C:\Program
> Files\R\R-2.2.0\bin\Rgui.exe" --sdi  --max-mem-size=2000M" and (b) I
> have increased the virtual memory Total Page File size to 2000MB.  But
> it still runs out of memory.
> Help! Any suggestions -- I don't really have access to any bigger
> computers?

You don't need a bigger computer, you need more RAM, which is pretty 
cheap these days. I can't imagine it would take more than 512 Mb to do 
16 U133 plus 2 chips, so you might look into adding a 512 Mb stick.



> Thanks.
> ---Nick
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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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