[BioC] running out of memory

[Carlos J. Gil Bellosta]

Hello,

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

Regards,

Carlos J. Gil Bellosta
http://www.datanalytics.com

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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