Read the error message.  The following tasks will help see how to solve the
problem

> library(Biobase)
> data(sample.ExpressionSet)
> sampleNames(sample.ExpressionSet)
 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R"
"S"
[20] "T" "U" "V" "W" "X" "Y" "Z"
> sampleNames(assayData(sample.ExpressionSet))
 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R"
"S"
[20] "T" "U" "V" "W" "X" "Y" "Z"
> sampleNames(phenoData(sample.ExpressionSet))
 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R"
"S"
[20] "T" "U" "V" "W" "X" "Y" "Z"
> sampleNames(phenoData(sample.ExpressionSet))[1] = "ZZ"
> validObject(sample.ExpressionSet)
Error in validObject(sample.ExpressionSet) :
  invalid class "ExpressionSet" object: 1: sampleNames differ between
assayData and phenoData
invalid class "ExpressionSet" object: 2: sampleNames differ between
phenoData and protocolData
> sampleNames(phenoData(sample.ExpressionSet))[1] = "A"
> validObject(sample.ExpressionSet)
[1] TRUE

You need, and the above code shows you have convenient facilities for,
achieving agreement in sample names for two components of your expression
data -- the assayData and the sample-level "phenoData".  It is critical that
these names be appropriate to both facets of the expression data, thus the
object validator fails when discrepancies are noted.  Whence the
discrepancies arose is not discernible from your notes.

> sessionInfo()
R version 2.11.0 Patched (2010-05-01 r51901)
x86_64-apple-darwin10.3.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] affy_1.26.0     Biobase_2.8.0   weaver_1.14.0   codetools_0.2-2
[5] digest_0.4.2

loaded via a namespace (and not attached):
[1] affyio_1.16.0         preprocessCore_1.10.0


On Wed, May 5, 2010 at 11:27 AM, Dirk Swanevelder <
dirk.swanevelder@googlemail.com> wrote:

> 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]]
>
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>

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