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 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099

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 days. Dick Beyer <dbeyer@u.washington.edu> Sent by: bioconductor-bounces@stat.math.ethz.ch 09/08/03 01:50 PM To: Bioconductor <bioconductor@stat.math.ethz.ch> cc: 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, Dick ********************************************************************** ********* 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor [[alternative HTML version deleted]]

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 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

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. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Dick Beyer <dbeyer@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, Dick ********************************************************************** ********* 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor