[BioC] Problem with R-2.5.1 on SuSE 10.1

[Kasper Daniel Hansen]

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