[BioC] running out of memory

[James W. MacDonald]

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).

Best,

Jim


> 
> Any other tips?
> Thanks,
> Javier
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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