[BioC] ExpressionSet error message: "featureNames differ"

Jobin K. Varughese jobinv at gmail.com
Sat Nov 16 13:25:17 CET 2013

Hello. My name is Jobin K. Varughese MD PhD, and I work at the University
of Bergen, Norway.

My issue is that I am having trouble with the ExpressionSet class. It
appears when running the following command (adapted from the

> library(shRNAseq)
> dataPath <- ".."
> x <- loadReadCounts(
+   screenData="phenoData.txt",
+   shRNAData="shRNALibrary.txt",
+   condition1="raw_tmz.txt", condition1Name="TMZ",
+   condition2="raw_ctrl.txt", condition2Name="Control",
+   dataPath=dataPath)

Error in validObject(.Object) :
  invalid class “shrnaSet” object: featureNames differ between
assayData and featureData

I've made sure that the featureNames are indeed identical between the
various files. Next, I tried contacting the developer of shRNAseq and even
sent him my raw data files. He attempted several strategies to solve the
issue: *"I've changed the names in the first columns to numbers 1:27500 and
made sure they match exactly between the files - didn't help. I've checked
line endings (Mac/Unix/Windows) - didn't help. I've removed the final blank
lines - didn't help. I've stripped quotes - didn't help."*

Eventually he also was unable to get past the error message, but could
provide the following: *"The shRNAset object is basically an expression set
(Eset) and the methods are inherited from that (including the error

The error is reproducible with the sample files that I've attached
(compressed with 7zip). I have also attached the output from sessionInfo()
and traceback().

Can anyone advise me as to what might be the problem? I would be very
grateful indeed.

Jobin K. Varughese

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