[BioC] RE : memory problem to read CEL files

[Simon Noël]

Hi,

I already get that problem under windows.  There a function to increase memory that windows can use.  I put it with an if to detect the OS so it don't cause any error if you run it under linux or windows because the function to allocate memory only work under windows.  So now, every R script I create automatically contain those line.

#Allocate memory under windows
if (.Platform$OS.type == "windows") 
{
    memory.limit(size = 4095)
    memory.limit()
}

Simon Noël
CdeC
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Lenka Radova [avodar at gmail.com]
Date d'envoi : 30 mars 2011 14:29
À : bioconductor at r-project.org
Objet : Re: [BioC] memory problem to read CEL files

Hi,
try

data <- justRMA()

it will give you the same final data as

data1<- ReadAffy()
data<-rma(data1)

Lenka


2011/3/30, Steve Lianoglou <mailinglist.honeypot at gmail.com>:
> Hi,
>
> On Wed, Mar 30, 2011 at 10:35 AM, Xiaobin Yuan
> <xiaobin.yuan at louisville.edu> wrote:
>> Dear list,
>>
>> My colleague can not read some cel files. There 24 CEL files.  Each
>> file has the size of 13M.   The following is the error message:
>>
>> data<-ReadAffy()
>> Error: cannot allocate vector of size 248.1 Mb
>>
>> If only put 12 files in the directory, R can read it without error.
>> Does anyone has this problem before?
>>
>> Those files can be read in my computer. And the size of  RAM  is the
>> same for our computers.
>
> Somehow your colleague has access to less of the RAM than you do ...
> is he running other programs? Is he running R in 32 bit mode?
>
> Another thing to consider is looking at the aroma-project if you have
> more microarrays than your cpu does RAM:
> http://www.aroma-project.org/
>
> -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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