Hello again. I was informed that I should share this as a public Dropbox
link rather than as an attachment. This link can be found here:
https://dl.dropboxusercontent.com/u/6322354/ExpressionSet_error.zip

Thank you.

Jobin


On Sat, Nov 16, 2013 at 1:25 PM, Jobin K. Varughese <jobinv@gmail.com>wrote:

> 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
>

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