Error in validObject(.Object) : invalid class “ExpressionSet” object: sampleNames differ between assayData and phenoData
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6 weeks ago
Chris ▴ 260

Hi Biostar,

I try to perform Differential expression at pathway level:

 disease_es <- gsva(disease_Par)

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

https://bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.html
Seem the error is because the colnames(gene_expression) is not in the same or order of rownames(p_Data). I found an similar issue here: https://support.bioconductor.org/p/84162/
Would you please have a suggestion to fix this error? Thank you so much!

With some manipulate the name, I reordered it to match and no more error.

GSVA • 393 views
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