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.