[BioC] Memory problems with normalize.AffyBatch.quantiles

[James MacDonald]

There appears to be a problem with this function, in particular the C
code (qnorm_c). I run out of memory on a WinXP box with 2Gb ram when I
try to normalize only 9 (!) affy U-133A chips. I can do 8, but at 9 I
get   Error: cannot allocate vector of blahblah kb

I ran the debugger on normalize.quantiles, and it blows up right after
passing the matrix to the C code.

R: 1.7.1
Affy 1.3.4
WinXP
2 Gb RAM

I don't have this problem (at least with these 9 chips) on the same box
running Linux (R 1.7.1, Affy 1.3.4), so maybe it is a Windoze problem?

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