[BioC] Re: Affy cel file processing - system requirements

[James MacDonald]

I would rank importance in this order:
1.) RAM
2.) OS
3.) Processor speed

512 Mb of RAM is probably too little for any reasonable number of
chips, so you are probably running out of memory. If you are using R <
devel, then you may be having malloc problems. If you can compile
R-devel (or simply download from Duncan Murdoch's web page), this will
help with memory allocation of large objects. First off, however, I
would get another 512 Mb (or better yet, another 1 Gb) of RAM.


Best,

Jim


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

>>> Francois Collin <fcollin at sbcglobal.net> 01/08/04 10:55AM >>>
Dear list:
I know this has been discussed before, but I can't open the link to the
 Bioconductor Archives. 
My question is regarding the key system requirements to be able to
"comfortably" analyze Affy cel files.  The bottleneck on my machine
(more like a dead end) is trying to run bg.adjust.gcrma().  I'm running
Windows 2000, on a Pentium 4 CPU 1.80GHz with 526M of RAM.  Is there
informed opinion on the relative importance of the various factors?
Operating  system: Windows vs Linux/Unix?
Speed of Processor?
Memory capacity?
Other factors?
 
Thanks
 
-francois


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