Problem with R-2.5.1 on SuSE 10.1
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Weigong Ge ▴ 10
@weigong-ge-2395
Last seen 11.3 years ago
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@kasper-daniel-hansen-2979
Last seen 2.5 years ago
United States
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
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