Re: [R] Memory allocation

From: James W. MacDonald <>
Date: Thu 13 Oct 2005 - 03:23:23 EST

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 (

To answer your question, there are several possibilities.

1.) Get more RAM (if on windows, start R with --max-mem-size=<amount of RAM>) 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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Received on Thu Oct 13 03:29:57 2005

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