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

FCollin at genelogic.com FCollin at genelogic.com
Mon Sep 8 14:55:59 MEST 2003

It takes a long time, definitely more than 20 minutes.    I never timed it 
as I usually let it run overnight, but it's on the order of hours, not 

Dick Beyer <dbeyer at u.washington.edu>
Sent by: bioconductor-bounces at stat.math.ethz.ch
09/08/03 01:50 PM

        To:     Bioconductor <bioconductor at stat.math.ethz.ch>
        Subject:        [BioC] how long to calculate gcrma on 16 arrays?

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,
Richard P. Beyer, Ph.D.          University of Washington
Tel.:(206) 616 7378              Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696              4225 Roosevelt Way NE, # 100
                                                 Seattle, WA 98105-6099

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