[BioC] ExpressionSet error message: "featureNames differ"

[Jobin K. Varughese]

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
shRNAseq<http://rock.icr.ac.uk/software/shrnaseq.jsp>vignette):

> 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
message)."*

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.

Sincerely,
Jobin K. Varughese