[BioC] Reading 80 CEL files.

[Michal Blazejczyk]

Hi,

Yeah, typical...

Try using function just.rma instead of calling ReadAffy.
just.rma operates directly on files and requires way less
memory.

Or run it on Linux, I think there's less memory issues
there.

Good luck,

Best,
Michal Blazejczyk
FlexArray Lead Developer
http://genomequebec.mcgill.ca/FlexArray/


> 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 = ¡šD://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