R help - Oct 2005 - 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.

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?

-- 
Rodney A. Staggs
Cancer Center Informatics Shared Resource
425 Delaware St S.E. MMC 806
University of Minnesota
Minneapolis, MN  55455
 
Office: Room B532 Mayo
Telephone: (612)624-2445
Email: stagg004 at umn.edu

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