[R] memory limit

[Martin Morgan]

On 05/08/2010 10:00 AM, Uwe Ligges wrote:
> 
> 
> On 08.05.2010 18:52, Zoppoli, Gabriele (NIH/NCI) [G] wrote:
>>
>> Hi,
>>
>> when I try to import a microarray CEL batch, I get this error message:
>>
>>> myAB<- ReadAffy ()
> 
> This seems to be more related to the BioC mailing list.

yes

  http://bioconductor.org/docs/mailList.html

and depending on the size of the problem

  > library(affy)
  > ?justRMA

or other solutions (e.g., the aroma.light and related packages),
depending on the number of CEL files you're processing.

Martin
> 
> 
>> Error in .Call("read_abatch", filenames, rm.mask, rm.outliers,
>> rm.extra,  :
>>    cannot allocate vector of length 1287151200
> 
> This indicates that the problem is the number of elements rather than
> the amount of RAM in the first place.
> 
> 
>> which, assuming the value is in bites, is below my RAM values (3 Gb
>> recognized by Windows).
> 
> Probably this is 32-bit R under 32-bit Windows? See ?Memory regarding
> the restrictions here....
> 
> Uwe Ligges
> 
> 
>>
>> The isse is, when I try to do
>>
>>   memory.limit (size =   3000 )
>>
>> the error doesn't resolve, and when I type
>>
>>> memory.size ()
>>
>> I always get
>> [1] 26.85
>>
>> I'm confused here. Can anybody help me?
>>
>> Thanks!
>>
>> Gabriele Zoppoli, MD
>> Ph.D. Fellow, Experimental and Clinical Oncology and Hematology,
>> University of Genova, Genova, Italy
>> Guest Researcher, LMP, NCI, NIH, Bethesda MD
>>
>> Work: 301-451-8575
>> Mobile: 301-204-5642
>> Email: zoppolig at mail.nih.gov
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793