[BioC] running out of memory

Carlos J. Gil Bellosta cgb at datanalytics.com
Wed Jan 20 17:36:37 CET 2010


How big are your 100 CEL files in total? At what point does it break?
Just at the normalization step?


Carlos J. Gil Bellosta

El día 20 de enero de 2010 17:24, Javier Pérez Florido
<jpflorido at gmail.com> escribió:
> Dear Steve,
> Thanks for your help, but, I'm trying to preprocess using RMA, GCRMA, VSN
> and dChip methods and I don't see any function in aroma.affymetrix that
> performs the whole preprocessing...
> Steve Lianoglou escribió:
>> 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
>> HTH,
>> -steve
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