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Dirk Swanevelder
▴
10
@dirk-swanevelder-4063
Last seen 10.5 years ago
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.nam
es=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
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