Question: Expressionset Error Message
0
gravatar for jobinv
6.8 years ago by
jobinv1.1k
Bergen, Norway
jobinv1.1k wrote:

I seem to be getting a strange error message when I run this command:

> library(shRNAseq)
> dataPath <- "../output"
>
> x <- loadReadCounts(
+   screenData="phenoData.txt",
+   shRNAData="../raw_data/shRNALibrary.txt",
+   condition1="raw_tmz.txt", condition1Name="TMZ",
+   # condition1="raw_hpx.txt", condition1Name="Hypoxia",
+   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)."

Perhaps someone here could suggest what my next step could be? For example, where would be a better place to ask this question?

PS: he also suggested that I make some sample datasets and test with that, so I am in the process of doing that.

• 2.3k views
ADD COMMENTlink modified 6.7 years ago • written 6.8 years ago by jobinv1.1k
1

In general, a reproducible example is the place to start, but you'll likely have to work with the developer on this. If the developer would like help troubleshooting, he/she should consider sharing the example on the bioconductor devel email list. As an aside, the best place to post questions about bioconductor is on the bioconductor email list.

ADD REPLYlink written 6.8 years ago by Sean Davis26k

Thanks for the tip!

ADD REPLYlink written 6.7 years ago by jobinv1.1k
1
gravatar for jobinv
6.7 years ago by
jobinv1.1k
Bergen, Norway
jobinv1.1k wrote:

The solution, as provided by Martin Morgan, was to make a version of shRNALibrary.txt where shRNALibrary$Label <- make.names(shRNALibrary$Label), due to a bug in the package. See more details here: https://stat.ethz.ch/pipermail/bioconductor/2013-November/056100.html

The developers have been informed about the bug.

ADD COMMENTlink written 6.7 years ago by jobinv1.1k
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