What's your sessionInfo()?
I also wonder if you do have all the 3GB available at the moment
you're running snprma().
And just to make sure I didn't misunderstand, are you reading in only
one file?
thank you,
b
On May 25, 2007, at 2:37 PM, Brandon Higgs wrote:
> 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
