I am trying to use juastGCRMA, but am running into a problem part way through the calculation: mydata.gcrma <- justGCRMA(filenames=rownames(pData(pd.heart)), phenoData=pd.heart, optimize.by=c(,"memory"), type = c("fullmodel")) Computing affinities..Done. Error in all(arg == choices) : Argument is missing, with no default The one argument I did not specify was "compress". I have a mix of both compressed and uncompressed files. (ReadAffy handles that case.) I did try this with only uncompressed files, but still got the same error message. I am running on windows 2000, with R 1.9.0 beta 3/27 build. base 1.9.0 utils 1.9.0 graphics 1.9.0 stats 1.9.0 methods 1.9.0 gcrma 1.0.6 affy 1.4.21 Biobase 1.4.10 tools 1.9.0 splines 1.9.0 matchprobes 1.0.2 mgu74av2cdf 1.4.3 mgu74av2probe 1.0 I'd greatly appreciate any help or suggestions. Thanks very much, 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

Your call to optimize.by is wrong. Instead of optimize.by=c(,"memory") use optimize.by="memory". Best, 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> 04/07/04 07:56PM >>> I am trying to use juastGCRMA, but am running into a problem part way through the calculation: mydata.gcrma <- justGCRMA(filenames=rownames(pData(pd.heart)), phenoData=pd.heart, optimize.by=c(,"memory"), type = c("fullmodel")) Computing affinities..Done. Error in all(arg == choices) : Argument is missing, with no default The one argument I did not specify was "compress". I have a mix of both compressed and uncompressed files. (ReadAffy handles that case.) I did try this with only uncompressed files, but still got the same error message. I am running on windows 2000, with R 1.9.0 beta 3/27 build. base 1.9.0 utils 1.9.0 graphics 1.9.0 stats 1.9.0 methods 1.9.0 gcrma 1.0.6 affy 1.4.21 Biobase 1.4.10 tools 1.9.0 splines 1.9.0 matchprobes 1.0.2 mgu74av2cdf 1.4.3 mgu74av2probe 1.0 I'd greatly appreciate any help or suggestions. Thanks very much, 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hi Jim, Thank you for pointing out my obvious syntax mistake. I used the correct syntax and all worked well. 48 mgu74av2 chips, a mix of compressed and uncompressed, took about 5 minutes. Sorry to have bothered you and everyone with such a trivial problem. Thanks very much for your help, 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 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ********************************************************************** ********* On Thu, 8 Apr 2004, James MacDonald wrote: > Your call to optimize.by is wrong. Instead of optimize.by=c(,"memory") > use optimize.by="memory". > > Best, > > 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> 04/07/04 07:56PM >>> > I am trying to use juastGCRMA, but am running into a problem part way > through the calculation: > > mydata.gcrma <- justGCRMA(filenames=rownames(pData(pd.heart)), > phenoData=pd.heart, optimize.by=c(,"memory"), type = c("fullmodel")) > Computing affinities..Done. > Error in all(arg == choices) : Argument is missing, with no default > > The one argument I did not specify was "compress". I have a mix of > both compressed and uncompressed files. (ReadAffy handles that case.) > > I did try this with only uncompressed files, but still got the same > error message. I am running on windows 2000, with R 1.9.0 beta 3/27 > build. > > base 1.9.0 > utils 1.9.0 > graphics 1.9.0 > stats 1.9.0 > methods 1.9.0 > gcrma 1.0.6 > affy 1.4.21 > Biobase 1.4.10 > tools 1.9.0 > splines 1.9.0 > matchprobes 1.0.2 > mgu74av2cdf 1.4.3 > mgu74av2probe 1.0 > > I'd greatly appreciate any help or suggestions. > > Thanks very much, > 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 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >