Hello Dear BioC,

I am working with affymetrix PorGene 1.0 ST arrays and are trying to read in my CEL files with the oligo package. I  am in trouble integrating the phenodata to the expression data. the code i am trying...

 The pData.txt is the file with my phenodata.

> pheno <- read.AnnotatedDataFrame("pData.txt", header = TRUE, row.name="Filename",sep="\t")
Error in data[[rowvar]] : attempt to select less than one element
> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pheno, verbose = TRUE)
Platform design info loaded.
Error in data[[rowvar]] : attempt to select less than one element
> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pheno, verbose = TRUE)
Platform design info loaded.
Reading in : 0h_rep1_(PorGene-1_0-st).CEL
Reading in : 0h_rep1_(PorGene-1_0-st).CEL
Reading in : 0h_rep2_(PorGene-1_0-st).CEL
Reading in : 0h_rep2_(PorGene-1_0-st).CEL
Reading in : 0h_rep3_(PorGene-1_0-st).CEL
Reading in : 0h_rep3_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep1_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep1_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep2_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep3_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep2_(PorGene-1_0-st).CEL
Reading in : 24hp_vacci_rep3_(PorGene-1_0-st).CEL
Error in validObject(out) : invalid class “GeneFeatureSet” object:
  NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see
    ?"channelNames<-,NChannelSet,character-method"
> x <- varMetadata(pheno)
Error in validObject(out) : invalid class “GeneFeatureSet” object:
  NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see
    ?"channelNames<-,NChannelSet,character-method"
> x <- varMetadata(pheno)
> x <- data.frame(x, channel = "_ALL_")
> varMetadata(pheno) <- x
> eset <- rma(oligoRaw)
Error in probeNames(object, subset) :
  error in evaluating the argument 'object' in selecting a method for function 'probeNames': Error: object 'oligoRaw' not found
> x <- data.frame(x, channel = "_ALL_")
> varMetadata(pheno) <- x
> eset <- rma(oligoRaw)
Error in probeNames(object, subset) :
  error in evaluating the argument 'object' in selecting a method for function 'probeNames': Error: object 'oligoRaw' not found

Please advice me..how could proceed?

Greetings and cheers!

Amin

There is likely something wrong with the phenoData that you are trying to load. It's fairly tricky to create a correct phenoData object, so try without it first.

oligoRaw <- read.celfiles(list.celfiles())

eset <- rma(oligoRaw)