I'm having memory issues on a linux machine with 3GB RAM with the oligo package for 550K arrays.  I'm trying to extract intensities and genotype calls from the cels, but can't seem to get past snprma().  My code is below.  Any thoughts are greatly appreciated.


> celpath <- /home/celfiles"
> fns <- sort(list.celfiles(path=celpath,full.names=TRUE))
> x <- read.celfiles(filenames=fns,verbose=T)
Incompatible phenoData object. Created a new one.
Creating objects outside R to store intensities.
This may take a while... Done.
Now reading CEL files
Reading in : /export/home/bhiggs/snp/stanley/XX_1_nsp.CEL
 Done.
Platform design info loaded.
> y <- snprma(x)
Error: cannot allocate vector of size 921.7 Mb

-B


 
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