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

James MacDonald jmacdon at med.umich.edu
Tue Sep 9 09:29:14 MEST 2003

I have not run gcrma with these particular chips, but when I run with
U133A chips, it takes probably 30 minutes for 8 arrays. This is on a 2.4
GHz P4 with 2 Gb RAM running WinXP.


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Dick Beyer <dbeyer at u.washington.edu> 09/08/03 04:50PM >>>
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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