The invalid class “ExpressionSet” object: sampleNames differ between phenoData and protocolData error occurs whenever the row names of the phenodata file does not match the names of the CEL files. The order of the samples in the phenoData file also matters.

One way to check if they match is to pass the phenoData instance created with the AnnotatedDataFrame method to the pData function.
>pData(phenodatainstance);

and pass the AffyBatch object produced by a Readaffy or read.celfiles function to the sampleNames function, as shown below:

> sampleNames(affydata);

The number, order and string values returned by both statements should match.


Manuel X. Duval, PhD
University of New Haven
Biology Adjunct
Biological Sciences
mduval@newhaven.edu
Cell: 860-287-3570


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