Question: baySeq pairedData error
0
gravatar for amab424
3.6 years ago by
amab4240
amab4240 wrote:

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 • 612 views
ADD COMMENTlink modified 3.6 years ago by Thomas J Hardcastle180 • written 3.6 years ago by amab4240
Answer: baySeq pairedData error
0
gravatar for Thomas J Hardcastle
3.6 years ago by
United Kingdom
Thomas J Hardcastle180 wrote:

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

ADD COMMENTlink written 3.6 years ago by Thomas J Hardcastle180
Answer: baySeq pairedData error
0
gravatar for amab424
3.6 years ago by
amab4240
amab4240 wrote:

Thanks Tom,

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

ADD COMMENTlink written 3.6 years ago by amab4240

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

ADD REPLYlink written 3.6 years ago by Thomas J Hardcastle180
Answer: baySeq pairedData error
0
gravatar for amab424
3.6 years ago by
amab4240
amab4240 wrote:

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)))

ADD COMMENTlink written 3.6 years ago by amab4240
Answer: baySeq pairedData error
0
gravatar for Thomas J Hardcastle
3.6 years ago by
United Kingdom
Thomas J Hardcastle180 wrote:

Ok - it's the example that is out of date.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

 

ADD COMMENTlink written 3.6 years ago by Thomas J Hardcastle180
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