[BioC] justRMA() execution problems

James MacDonald jmacdon at med.umich.edu
Fri Feb 13 01:13:49 MET 2004

The plus2 chips are more than twice the size of the old 133A chips, so I
would guess you are running out of memory (I can do ~100 of the 95A
chips with 512 Mb of RAM, but I get really close to bombing out).
Normally you would get a message saying R was not able to allocate a
vector of xxxx bytes, but it might be that you are running out of memory
during a call to C code, and that is causing the crash. Ben Bolstad
would be more likely to know if that is what is happening.

Anyway, RAM is pretty cheap these days so if you are going to be working
with that many of the Plus2 chips, you might want to get some more.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Srikanth <sjammula at myriad.com> 02/12/04 4:38 PM >>>
I am trying to run justRMA() in R1.8.1 on 110   hgu133plus2 cel files on

a Windows 2000 machine with 1 GB RAM, 3.0 GHz processor.

I increased the memory allocation with the command memory.limit(1700)

It runs for about 10 minutes with the CPU usage almost maxed out, then 
says "background correcting" at which point, the CPU usage for Rgui.exe 
comes down to about 4 % and the memmory usage goes up.

Soon after that I get a box that says RGui.exe has generated internal 
errors and will be closed down and the application quits.

I would appreciate any help on this.

Srikanth Jammulapati

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