[BioC] running out of memory

James W. MacDonald jmacdon at med.umich.edu
Wed Jan 20 17:26:36 CET 2010

Hi Javier,

Javier Pérez Florido wrote:
> Dear list,
> I'm trying to normalize using threestep several CEL files (around 100 
> CEL files). I got the following error:
> Error: cannot allocate vector of size 6.5 Mb
> I've been reading the suggestions about this error in the mailing list, 
> but I couldn't fix it. My system (Win XP Prof, 32 bits) has 3 GB RAM and 
> I did the following:
>     * I used the command line --max-mem-size=3071M in the R shortcut
>     * I changed the boot.ini file to allow up to 3GB
>           o [boot loader]
>             timeout=30
>             default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
>             [operating systems]
>             multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft
>             Windows XP Professional" /3GB /noexecute=optin /fastdetect
>     * I try to remove not used variables using the rm() command and the
>       garbage collector gc() within the source code.
> But, even with those changes, I'm still running out of memory. It is 
> strange, because, having a look at the tasks administrator, R doesn't 
> use more than 1600 MB and the whole system never goes further than 2GB

You won't be able to normalize 100 chips with 3 Gb RAM. If you really 
want to use threestep(), you will either have to come up with a 64 bit 
computer with more memory, or as Steve Lianoglou mentioned, use 
aroma.affymetrix (which IIRC includes routines from affyPLM).



> Any other tips?
> Thanks,
> Javier
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

More information about the Bioconductor mailing list