DEXSeq error while creating ExonCountSet object

[dpryan]

Cross-posted on biostars, where I already answered.

[onthefly]

Hi

I am using DEXSeq for my analysis.

However, I am facing error while making the ExonCountSet object for further processing.

Specifically, on running

ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, dros_flattened.gff)

I get the error:

Error in checkAtAssignment("character", "annotationFile", "character") :
  ‘annotationFile’ is not a slot in class “character”
In addition: Warning message:
'newExonCountSet' is deprecated.
Use 'DEXSeqDataSet' instead.
See help("Deprecated")

I prepared the gff file using the dexseq python script, and all other steps also as in the DEXSeq vignette.

Any suggestions/workarounds are most welcome.

Thanks

M