[BioC] Question on GCRMA

[Francois Pepin]

Hi Hegang,

This is happening because you're running out of memory. 

Using justGCRMA instead of GCRMA should help solve your problem. R is
kind of bad at memory management and the justGCRMA function is coded in
C to get around this.

Otherwise you could also try to work on a computer with more RAM, but
keep in mind that windows has limitation as to how much memory can be
used.

There also is a lot of discussion in the list archives if you want more
details.

hope this helps,

Francois

On Thu, 2006-11-02 at 10:46 -0800, Henry Chen wrote:
> Hi all,
>    
>   I have faced a problem on running GCRMA.
>   I have 67 chips of hgu133plus2 and try to calculate expression measures
>   and normalize them by GCRMA. However, there is an error as
>   follows
>    
>   "Adjusting for optical effect..Error: cannot allocate vector of size 297408 Kb"
> 
>   Does anyone know how to solve this problem. Thanks!
>    
>    
> 
> 
> Hegang H. Chen, Ph.D.
> Associate Professor
> Division of Biostatistics and Bioinformatics
> Dept of Epidemiology and Preventive Medicine
> University of Maryland School of Medicine
> 660 W. Redwood
> Baltimore, MD 21201
> U.S.A.
>  
> ---------------------------------
> 
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> 
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