[BioC] gcrma and memory size - rhdf5 question

[James MacDonald]

1.) Put --max-mem-size=2500M in the target field for the shortcut you
use to start R (after the ...RGui.exe part). Theoretically a 32 bit
machine can use 4 GB RAM, but Windoze takes a bunch, so the true limit
is something less than 4 GB. I think the patched version uses a better
memory allocation scheme than 1.8.0, and for sure 1.9.0 pre-release
does, so you might want to compile that one up and try it.

2.) To use rhdf5, you have to get the hdf5.dll first and then compile
the package. There was a conversation about this on R-help yesterday
that you might want to look at.

http://finzi.psych.upenn.edu/R/Rhelp02/archive/0816.html

HTH,

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

>>> <Phguardiol at aol.com> 12/02/03 11:07AM >>>
Hi 
I m trying to use GCRMA 1.0.1 under R1.8.1 with Affy 1.3.26 under win
XP Pro with 18 U133A Affychips and I obtain this message:
background correcting...Error: cannot allocate vector of size 96 Kb
which means that I dont have enough RAM
How can I increase the memory size... knowing that I already have 3.62
Go RAM !!!
rhdf5 is not anymore available as a Win package...just as a source
package: could it be of some help here ? If so can somebody send me the
compiled version for Win ?
Is there a GCRMexpress version such as the RMAexpress that does not
need R ?
Should I move to a 1.4.x version of Affy ?
thanks for your precious help as usual
Philippe

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