[Bioc-devel] lumiT VST Normalisation Fails

Dario Strbenac dstr7320 at uni.sydney.edu.au
Fri Nov 1 07:00:18 CET 2013


I have a LumiBatch object, but the lumiT function produces an error.

> class(treatmentBatch)
[1] "LumiBatch"
[1] "lumi"
> treatmentBatch <- lumiT(treatmentBatch)
Perform vst transformation ...
Error in !assayDataValidMembers(assayData(x.lumi), "detection") :
  invalid argument type

Since I've created a valid object of class LumiBatch, it should work on that object without errors. In fact, the documentation of the class states : "The arguments to new should include exprs and se.exprs, others can be missing, in which case they are assigned default values." Nothing in the documentation of lumiT states that detection p-values are required, so it's a mystery to the lumi end-user what obscure format of parameters the package author expects them to provide.

Another example of this type of problem is 

> treatmentBatch <- addControlData2lumi(controlTable, treatmentBatch)
Error in addControlData2lumi(controlTable, treatmentBatch) :
  SampleID does not match up between controlData and x.lumi!

controlData is described as "a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the expression amplitudes for individual samples." Searching the entire PDF manual of the help pages also does not show SampleID described anywhere.

I am using lumi 2.14.0.

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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