[BioC] snprma for 500K array

Benilton Carvalho bcarvalh at jhsph.edu
Fri May 25 23:23:08 CEST 2007

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,


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

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