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Hi Loren, Loren Engrav wrote: > I have R and Bioconductor and X11 and tkWidgets and widgetTools working on > Mac OS 10.4.8 We need more information than that. What is the ouput from sessionInfo()? > > I enter > >>library(affy) > > > And then > >>mydata <- ReadAffy(widget=TRUE) > > > And then get > > Error in new.env(hash = TRUE, parent = NULL) : > use of NULL environment is defunct > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for signature > "NULL" > > Whereas if I enter > >>mydata <- ReadAffy() > > > All goes well > > How do I fix this? I wonder if you have a newer version of R with an old version of affy or Biobase. I am not on a Mac, so I can't test. However, it works for me on windows: > dat <- ReadAffy(widget=T) Loading required package: tkWidgets Loading required package: widgetTools Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: DynDoc > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tcltk" "tools" "stats" "graphics" "grDevices" "utils" "datasets" [8] "methods" "base" other attached packages: tkWidgets DynDoc widgetTools affy affyio Biobase "1.12.1" "1.12.0" "1.10.0" "1.12.2" "1.2.0" "1.12.2" Best, Jim > > Thank you > > > ---from > > ...all creatures great and small... > > Loren H. Engrav, MD > Professor, Division of Plastic Surgery > Harborview Med Ctr, 359796 > 325 Ninth Avenue > Seattle, WA 98104 > office 206 731 3209 > fax 206 731 3656 > email engrav at u.washington.edu > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.