[BioC] Memory error wihle processing 35 Affymetrix cel files

[James W. MacDonald]

Hi Gunther,

Gunther Höning wrote:
> Dear list,
> 
> currently I'm trying to process 35 cel-files of the Affymetrix Human U133
> Plus 2.0 chip.
> 
> I load the libraries and read the chips into an affybatch.
> Background correction works well but during normalisation I always receive:
> "Cannot allocate vector of size 352848...")
> 
> I am using openlinux 10.2 with 2 GB RAM.
> Does anyone know a solution to this problem ?
> Using more RAM ?

Unless you specifically need to do things stepwise, a simple

eset <- rma(chips)

should suffice. This should work fine with that much RAM.

Otherwise, yes. More RAM.

Best,

Jim


> 
> Gunther
> 
> Code:
> 
> library("affy") 		
> library("hgu133plus2probe")
> library("hgu133plus2cdf")
> chips <- ReadAffy()
> bg <- bg.correct(chips, method ="rma")
> norm <- normalize(bg, method ="quantiles")
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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