[R] Memory allocation

James W. MacDonald jmacdon at med.umich.edu
Wed Oct 12 19:23:23 CEST 2005

Rod Staggs wrote:
> I am trying to work with 75 affymetrix U133plus2 chips and am running into
> memory allocation errors when trying to merge or convert probe level data to
> expression values.

You don't say what package(s) you are using to do this, but assuming you 
are using the affy package, this is not the correct list - you should be 
using the BioC list (bioconductor at stat.math.ethz.ch).

To answer your question, there are several possibilities.

1.) Get more RAM (if on windows, start R with --max-mem-size=<amount of 

2.) Use justRMA()

3.) If on Windows, switch to *nix. The memory allocation is better, so 
you can analyze more chips with the same amount of RAM. Probably the 
easisest way to do this is with Quantian, which runs off a CD.



> I keep getting - Error: cannot allocate vector of size 561011 Kb and that is
> simply with a data subset.
> Is there a way around this limitation?

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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