Please ignore my previous submission. As Martin Morgan kindly pointed out to me, I was using an old version of simpleaffy. Updating to 2.8.0 eliminated my problem. Thanks, 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 http://staff.washington.edu/~dbeyer ********************************************************************** ********* > ------------------------------ > > Message: 9 > Date: Wed, 8 Nov 2006 14:15:59 -0800 (PST) > From: Dick Beyer <dbeyer at="" u.washington.edu=""> > Subject: [BioC] simpleaffy gives error: unable to find an inherited > method for function "pData" > To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: > <pine.lnx.4.43.0611081415590.12784 at="" hymn08.u.washington.edu=""> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > I've run into an error using simpleaffy on linux. I am running R in a > directory that contains several CEL files. > > library(simpleaffy) >> affyRaw <- ReadAffy() > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for > signature "phenoData" > >> sessionInfo() > R version 2.4.0 (2006-10-03) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > simpleaffy affy affyio Biobase > "2.2.0" "1.12.0" "1.0.0" "1.12.2" > > If I redo this without simpleaffy, then all is well. > > Thanks, > 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 > http://staff.washington.edu/~dbeyer >