Hi, I am having a problem using ReadAffy using the new AnnotatedDataFrame class: targets<-new("AnnotatedDataFrame") pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) Data<-ReadAffy(celfile.path =cel.path, filenames = sampleNames(targets), verbose=TRUE) Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : could not find function "read.AnnotatedDataFrame" I have the newest devel version of Biobase installed (see below) RSiteSearch("read.AnnotatedDataFrame") did not give me a result. Any idea what is wrong here or where I can find the requested function? Best, Georg > sessionInfo() R version 2.4.0 (2006-10-03) powerpc-apple-darwin8.7.0 locale: C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: maPlot maAnalysis hopach cluster geneplotter annotate "1.0" "1.0" "1.8.0" "1.11.2" "1.12.0" "1.13.2" affydata limma simpleaffy genefilter survival affy "1.10.0" "2.9.4" "2.9.0" "1.13.1" "2.29" "1.13.9" affyio Biobase "1.3.1" "1.13.13"

Hi Georg, Georg Otto wrote: > Hi, > > I am having a problem using ReadAffy using the new AnnotatedDataFrame class: > > targets<-new("AnnotatedDataFrame") > pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2) > > Data<-ReadAffy(celfile.path =cel.path, > filenames = sampleNames(targets), > verbose=TRUE) > > Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : > could not find function "read.AnnotatedDataFrame" > > I have the newest devel version of Biobase installed (see below) No, that version of Biobase is 0.0.06 versions old ;-D. The newest version is 1.13.19. Using an old version of R and devel versions of BioC packages is likely to result in these sorts of problems because you cannot easily use biocLite() to update things. I would recommend getting the newest version of Biobase, then getting the repos list, and then using update packages. a <- biocReposList() update.packages(repos=a, ask=FALSE) I'm not familiar with doing things on MacOS, but on windows adding a type="source" will usually work better because the binaries are sometimes not built, and usually take longer to propagate anyway. I assume you have to be set up to build source packages on MacOS as well? Also, RSiteSearch() doesn't search the BioC listserv. You have to go to the BioC website and click on the 'Join mailing list' link, then the link saying something about searchable archives provided by gmane. Best, Jim > > RSiteSearch("read.AnnotatedDataFrame") > > did not give me a result. > > Any idea what is wrong here or where I can find the requested function? > > Best, > > Georg > > > > >>sessionInfo() > > R version 2.4.0 (2006-10-03) > powerpc-apple-darwin8.7.0 > > locale: > C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > maPlot maAnalysis hopach cluster geneplotter annotate > "1.0" "1.0" "1.8.0" "1.11.2" "1.12.0" "1.13.2" > affydata limma simpleaffy genefilter survival affy > "1.10.0" "2.9.4" "2.9.0" "1.13.1" "2.29" "1.13.9" > affyio Biobase > "1.3.1" "1.13.13" > > _______________________________________________ > 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.