[BioC] Memory error wihle processing 35 Affymetrix cel files

[Adaikalavan Ramasamy]

James is correct. You could also try justRMA() in a fresh R session, 
preferably with minimal number of other programmes running in the 
background. Or ask a friend/collaborator who has access to a machine 
with more RAM or buy more RAM.

Regards, Adai



James W. MacDonald wrote:
> Hi Gunther,
> 
> Gunther Höning wrote:
>> Dear list,
>>
>> currently I'm trying to process 35 cel-files of the Affymetrix Human U133
>> Plus 2.0 chip.
>>
>> I load the libraries and read the chips into an affybatch.
>> Background correction works well but during normalisation I always receive:
>> "Cannot allocate vector of size 352848...")
>>
>> I am using openlinux 10.2 with 2 GB RAM.
>> Does anyone know a solution to this problem ?
>> Using more RAM ?
> 
> Unless you specifically need to do things stepwise, a simple
> 
> eset <- rma(chips)
> 
> should suffice. This should work fine with that much RAM.
> 
> Otherwise, yes. More RAM.
> 
> Best,
> 
> Jim
> 
> 
>> Gunther
>>
>> Code:
>>
>> library("affy") 		
>> library("hgu133plus2probe")
>> library("hgu133plus2cdf")
>> chips <- ReadAffy()
>> bg <- bg.correct(chips, method ="rma")
>> norm <- normalize(bg, method ="quantiles")
>>
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> 
>