Hi Everyone,



I'm having troubles with a script that previously worked after an upgrade to
the latest R and Bioconductor (2.6) versions. The "Rawdata.RData" is
produced. The else loop portion works, i.e. ReadAffy(), if the "Target.txt"
file is removed. The filenames are read from the Target file (tested).

* *

*> **base<-getwd()                                                         *

*>DATA<-paste(base,"/Raw and Normalized R datasets/",sep=""); DATA   *

*>dir.create(DATA,showWarnings=TRUE,recursive=FALSE)          *



*>if (file.exists("Target.txt")) {*

*
>pd<-read.AnnotatedDataFrame("Target.txt",sep="\t",header=TRUE,row.names=1);
*

*>data<-ReadAffy(filenames=pData(pd)$FileName);*

*>data@phenoData<-pd;*

*>save(data,file=paste(DATA,"Rawdata.RData",sep="")); } else {*

*>data<-ReadAffy()*

*>save(data,file=paste(DATA,"Rawdata.RData",sep="")) }*

*>esetRMA<-rma(data); *



Calculating Expression
Error in validObject(.Object) :
  invalid class "ExpressionSet" object: sampleNames differ between phenoData
and protocolData
Calls: rma ... callNextMethod -> eval -> eval -> .nextMethod -> validObject
Execution halted





*Target.txt file (tab delimited):*

SlideNumber FileName Target TechRep BioRep sampleNames
1 TUG 1.CEL 1 0 1 Tug1
2 TUG 2.CEL 1 0 2 Tug2
3 TUG 3.CEL 1 0 3 Tug3
4 TUG DN1_1.CEL 2 0 1 TugDn_1
5 TUG DN1_2.CEL 2 0 2 TugDn_2



*Libraries used in the script*

library(affy)

library(gcrma)

library(limma)

library(Biobase)

library(affyPLM)

library(marray)

library(annaffy)

library(geneplotter)

library(made4)

library(multtest)

library(vsn)

library(graphics)

library(IDPmisc)

Kind regards and many thanx for helping,

Dirk

	[[alternative HTML version deleted]]

