Hi,

I've just started playing with Bioconductor: I m trying to figure out a
problem I have with creating ExpressionSet from a text file containing
normalised microarray data:

exp = as.matrix(read.table("rma.txt", header=TRUE, sep="\t", row.names=1,
as.is=TRUE))
pd  = read.table("groups.txt", row.names= 1 , header = TRUE, sep="\t")
meta = data.frame(labelDescription = c("Age of patient"),
row.names=c("age"))
pheno = new("AnnotatedDataFrame", data=pd, varMetadata = meta)

works to here. but then it fails here:

my_set = new("ExpressionSet", exprs=exp, phenoData=pheno,
annotation="hgu133plus2")

Error in validObject(.Object) :
  invalid class "ExpressionSet" object: sampleNames differ between assayData
and phenoData

however when I do this:

m = new("ExpressionSet",exprs=exp)
phenoData(m)=  new("AnnotatedDataFrame", data=pd, varMetadata = meta)
annotation(m) = "hgu133plus2"

it works. What is the reason why it doesnt work/what am I doing wrong? I see
talk about se.expr but not sure how it all works together?

Nathan

	[[alternative HTML version deleted]]

