R help - May 2007 - Read in 250K snp chips

I'm having trouble getting summaries out of the 250K snp chips in R. 
I'm
using the oligo package and when I attempt to create the necessary SnpQSet
object (to get genotype calls and intensities) using snprma, I encounter
memory issues.

Anyone have an alternative package or workaround for these large snp chips?
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bhiggs wrote:
> I'm having trouble getting summaries out of the 250K snp chips in R. 
I'm
> using the oligo package and when I attempt to create the necessary SnpQSet
> object (to get genotype calls and intensities) using snprma, I encounter
> memory issues.
> 
> Anyone have an alternative package or workaround for these large snp chips?

Oligo is a Bioconductor package, so you should probably direct questions 
on the Bioconductor-help listserve rather than R-help.

Best,

Jim


-- 
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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