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

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

Thanks Tom,

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

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)))

Ok - it's the example that is out of date.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)