[BioC] Memory issue

Wolfgang Huber huber at ebi.ac.uk
Fri Apr 1 10:45:00 CEST 2005

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'.


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
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

More information about the Bioconductor mailing list