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This problem has been discussed at length on the email list before. The problem is that the se.exprs method does not exist anymore (which is a bit of a bummer in this case as the MAS5 P/A calls falls a bit outside of the normal paradigm). You need to replace se.exprs(SOMETHING) with something like assayData(SOMETHING, "se.epxrs") but do a search on the email list to find the exact syntax. Kasper On Sep 24, 2007, at 11:33 AM, Weigong Ge wrote: > Hello, > I have a problem when I run R on my Linux SuSE 10.1 show as below. > Does someone can give me help to fix it? > Thank you very much! > Weigong Ge > > wge at NCW04936:~> suPassword:NCW04936:/home/wge # sh /usr/local/ > tomcat/bin/startup.shUsing CATALINA_BASE: /usr/local/tomcatUsing > CATALINA_HOME: /usr/local/tomcatUsing CATALINA_TMPDIR: /usr/local/ > tomcat/tempUsing JRE_HOME: /usr/lib/jvm/java/jreNCW04936:/ > home/wge # R > R version 2.5.1 (2007-06-27)Copyright (C) 2007 The R Foundation for > Statistical ComputingISBN 3-900051-07-0 > R is free software and comes with ABSOLUTELY NO WARRANTY.You are > welcome to redistribute it under certain conditions.Type 'license > ()' or 'licence()' for distribution details. > Natural language support but running in an English locale > R is a collaborative project with many contributors.Type > 'contributors()' for more information and'citation()' on how to > cite R or R packages in publications. > Type 'demo()' for some demos, 'help()' for on-line help, > or'help.start()' for an HTML browser interface to help.Type 'q()' > to quit R. > [Previously saved workspace restored] >> library(affy)Loading required package: BiobaseLoading required >> package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' > and for packages 'citation(pkgname)'. > Loading required package: affyio> Data<-ReadAffy()> cdf=cdfName > (Data)> write(cdf,file="cdfname")> eset<-mas5(Data)background > correction: masPM/MM correction : masexpression values: > masbackground correcting...done.1031 ids to be > processed| ||####################|> calls<- > mas5calls(Data)Getting probe level data...Computing p-valuesMaking > P/M/A Calls> tb<-data.frame(exprs(eset),exprs(calls),se.exprs > (calls))Error in function (classes, fdef, mtable) : unable > to find an inherited method for function "se.exprs", for signature > "ExpressionSet"> > _________________________________________________________________ > > > [[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