Memory allocation

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