[BioC] how long to calculate gcrma on 16 arrays?

[Akil Merchant]

On my G4 power book rma on 16 mgu74av2 chips take less than 2 minutes.
I run R 1.7.1 on X11 for Mac OS X.

GC-RMA takes more than one hour.

Akil

On Monday, September 8, 2003, at 03:50  PM, Dick Beyer wrote:
> I have 16 mgu74av2 arrays.  When I do rma, it takes 45 seconds.  When  
> I do gcrma, it doesn't finish after 20 minutes.  How long should it  
> take?
>
>> ghrko.gcrma <- gcrma(ghrko.raw)
> Loading required package: mgu74av2probe
> Loading required package: matchprobes
> background correction: gcrma
> normalization: quantiles
> PM/MM correction : pmonly
> expression values: medianpolish
> background correcting...                <- gets stuck here
>
>
> I am running Windows 2000, R 1.7.1, biobase 1.3.29, affy 1.2.30, gcrma  
> 0.4.0, 2.8GHz dual Xeon, with 4GB RAM.
>
> Thanks for any help or suggestions,
> Dick
> *********************************************************************** 
> ********
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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