baySeq pairedData error
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amab424 • 0
@amab424-10135
Last seen 6.9 years ago

I'm trying to run baySeq but I'm getting this error:

Error in getClass(Class, where = topenv(parent.frame())) : 
  “pairedData” is not a defined class

 

Can someone help me with that.

 

Thanks

bayseq • 1.4k views
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@thomas-j-hardcastle-3860
Last seen 6.5 years ago
United Kingdom

You are using an old version of baySeq - please upgrade. The 'pairedData' class has been obsolete for several release cycles.

Alternatively, you are using an object created with an old version of baySeq in a newer version of baySeq. The easiest way to resolve this is usually to re-run the scripts which created the object. If this is problematic there are alternatives, but these are messy and require hacking about at the slot level of your objects.

Tom Hardcastle

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amab424 • 0
@amab424-10135
Last seen 6.9 years ago

Thanks Tom,

I'm not sure if the version what's causing the problem. I'm using baySeq_2.5.5

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That's odd, then. What command are you running that generates this error?

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amab424 • 0
@amab424-10135
Last seen 6.9 years ago

I tried this example data:

library(baySeq)
data(pairData)
pairCD <- new("pairedData", data = pairData[,1:4], pairData =
                pairData[,5:8],replicates = c(1,1,2,2),groups = list(NDE = c(1,1,1,1),  DE = c(1,1,2,2)))

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@thomas-j-hardcastle-3860
Last seen 6.5 years ago
United Kingdom

Ok - it's the example that is out of date. If you look at section 2 of the vignette at http://bioconductor.org/packages/devel/bioc/vignettes/baySeq/inst/doc/baySeq_generic.pdf you will find the current procedure for paired data analysis, which is to construct a countData object with a three-dimensional data structure; e.g.

pairCD <- new("countData", data = array(c(pairData[,1:4], pairData[,5:8]), dim = c(nrow(pairData), 4, 2)), replicates = c(1,1,2,2), groups = list(NDE = c(1,1,1,1), DE = c(1,1,2,2)), densityFunction = bbDensity)

 

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