[BioC] memory problem to read CEL files

[Martin Morgan]

On 03/30/2011 07:58 AM, Steve Lianoglou wrote:
> 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/

The functions just.rma in affy, just.gcrma (gcrma) are more memory 
efficient implementations for the common work flow from CEL to 
ExpressionSet via RMA / GCRMA.

Martin

>
> -steve
>


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