[BioC] running out of memory

Henrik Bengtsson hb at stat.berkeley.edu
Thu Jan 21 03:30:54 CET 2010

2010/1/20 Steve Lianoglou <mailinglist.honeypot at gmail.com>:
> Hi,
> 2010/1/20 Javier Pérez Florido <jpflorido at gmail.com>:
>> 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
> I can't really comment on tweaking memory settings on windows systems,
> but if all you're doing is trying to normalize a boat-load of affy
> arrays together, I understand that the aroma.affymetrix package can do
> so while keeping memory requirements down. Perhaps you might consider
> looking into it until someone can give you better advice:
> http://groups.google.com/group/aroma-affymetrix/web/overview

FYI, there is now a new web site (we'll remove the documentation from
the above soon):



> HTH,
> -steve
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
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