[BioC] Memory issue

[Wolfgang Huber]

Dear Salil,

how much memory does your machine have? How many files are there in 
"myfilenames" and what chiptypes are they? You might get started with 
using fewer arrays; on the long run, getting more memory seems like a 
good idea.

You can also try the justGCRMA (package gcrma) and justRMA functions: 
The man page says:
  This method should require much less RAM than the conventional
  method of first creating an 'AffyBatch' and then running 'gcrma'.

  Cheers
   Wolfgang



Salil wrote:
> Hi Group,
>  
> Iam a beginner in learning R and Bioconductor.
>  
> I have a basic question. 
> How can I increase the memory limit.
>  
> When I type the command:
>  
> abatch <- ReadAffy(filenames = myfilenames , phenoData = mypheno)
>  
> It throws me this error:
>  
> Error: cannot allocate vector of size 625759 Kb
> In addition: Warning message: 
> Reached total allocation of 511Mb
>  
>  
> How can I overcome this?
>  
> Thanks
> 

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber