[R] Memory allocation

[James W. MacDonald]

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 
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.


Best,

Jim



> 
> 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
734-647-5623