After reading CEL files importing phenotype data, i received an error message when trying rma(my data). the message says differing names of the CEL files between phenoData and protocolData. However I don't see any obvious difference in names. I pasted my flow below. The session is bolded. Your help is greatly appreciated. 

> GSE19804_data <- ReadAffy()
> pData(GSE19804_data)<-read.table("GSE19804_2_phenod.txt", header=T, row.names=1, sep="\t")
> GSE19804_eset <- rma(GSE19804_data)

Background correcting
Normalizing
Calculating Expression
Error in validObject(.Object) : 
  invalid class “ExpressionSet” object: sampleNames differ between phenoData and protocolData
> protocolData(GSE19804_data)
An object of class 'AnnotatedDataFrame'
  sampleNames: GSM494556.CEL GSM494557.CEL ... GSM494675.CEL (120 total)
  varLabels: ScanDate
  varMetadata: labelDescription
> phenoData(GSE19804_data)
An object of class 'AnnotatedDataFrame'
  sampleNames: GSM494556.CEL GSM494616.CEL ... GSM494675.CEL (120 total)
  varLabels: PatienID Diagnosis
  varMetadata: labelDescription

I think you have shown the problem yourself! Note that

> protocolData(GSE19804_data)
An object of class 'AnnotatedDataFrame'
  sampleNames: GSM494556.CEL GSM494557.CEL ... GSM494675.CEL (120 total)

has a different sample in the second position as compared to

> phenoData(GSE19804_data)
An object of class 'AnnotatedDataFrame'
  sampleNames: GSM494556.CEL GSM494616.CEL ... GSM494675.CEL (120 total)

thanks for your replies.

tried

all.equal(sampleNames(phenoData(GSE19804_data)), sampleNames(protocolData(GSE19804_data)))

receive

[1] "118 string mismatches"

seem there is a two mismatches although i made the pheno data file by pasting the names of CEL files.

i align the CEL files in a different order because i plan to run paired analysis. is that why?