Sorry for this question, but for some reason something is happening that I'm not able to find. I'm having the next problem while creating the expression set.

    pd <- data.frame(state = colnames(q@mat))
    rownames(pd) <- pd[,1]
    pd[,1] <- 1
    pheno = new("AnnotatedDataFrame", data=pd)
    x = q@mat 
    
    es =  ExpressionSet(assayData=x, phenoData = pheno)

I get

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

While it seems that they all have the same names in the same order.

> colnames(x) == rownames(pd)
  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [30] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [59] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 [88] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[117] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[146] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[175] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

If I add

colnames(x) <- rownames(pd)

to the code then I can run the script without any problem. Why?

Thanks for your time.

The validity test uses `identical()`, so you could try identical(colnames(x), rownames(pd)) and if that fails all.equal(colnames(x), rownames(pd)). I'd guess that one or the other (probably colnames(x)) has an attribute

> df = data.frame(x=1, row.names="a") 
> m = matrix(1, 1, 1, dimnames=list(NULL, "a"))
> e = ExpressionSet(m, AnnotatedDataFrame(df))
> colnames(m) = structure(colnames(m), foo="")
> colnames(m)
[1] "a"
attr(,"foo")
[1] ""
> e = ExpressionSet(m, AnnotatedDataFrame(df))
Error in validObject(.Object) : 
  invalid class "ExpressionSet" object: sampleNames differ between assayData and phenoData

Probably setting rownames on pd removes the attributes. FWIW it's better practice to use the constructor AnnotatedDataFrame() rather than new(); also all() would help summarize the test of equality.