[BioC] Reading 80 CEL files.

[olsen]

> 
> Hello~~~
> 
>  
> 
> I am trying to read 80 HG-U133A arrays so I did as
> follows:
> 
>  
> 
> > memory.limit(size=4095)
> 
> > options(object.size=10000000000, digits=8,
> scipen=100, memory=3200483647,
> contrasts=c("contr.treatment", "contr.poly"))
> 
> > library(affy)
> 
> > cel.file <- ReadAffy(celfile.path = ¡¨D://CEL)  
> 
>  
> 
> However, it showed
> 
>  
> 
> Error: cannot allocate vector of size 309.4 Mb
> 
>  
> 
> I have tried adding the --max-mem-size=2Gb tag onto
> my shortcut. 
> 
> The machine has 2G RAM and a 3.30GHz processor. 
> 
> Is there any idea to let R use more memory anywhere?
> 
> Thank you~
> 
>  
> 
> Best Regards,
> 
> Pure
> 
Pure,

My advice: run them in Linux. We have run up to 1000
arrays in a linux cluster.

Oscar Puig




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