[BioC] error in DEXSeq fitDispersionFunction()

Alejandro Reyes alejandro.reyes at embl.de
Mon Aug 13 13:12:14 CEST 2012

Dear Georg,

Sorry for the delay of my answer.
But yes, you have to generate the new ExonCountSet with the new version, 
or alternatively just do:

featureNames(ecs) <- paste(geneIDs, exonIDs, sep = ":")
rownames(counts(ecs)) <- featureNames(ecs)

Best wishes,

> Thanks a lot! Now unfortunately I get a problem at the the size factor 
> estimation step:
> > bat.counts <- estimateSizeFactors(bat.counts)
> Error in validObject(cds) :
> invalid class “ExonCountSet” object: The featureNames do not match 
> with the geneIDs:exonIDs
> Are there incompatibilities with the ExonCountSet object and the new 
> version of DEXSeq? Do I have to generate the ExonCountSet again with 
> the new version?
> Cheers,
> Georg
> On 07/08/12 23:06, Alejandro Reyes wrote:
>> Dear Georg,
>> Thanks for your email and noticing the error. A parameter of the 
>> glmnb.fit function (statmod package) changed recently from "start" to 
>> "coef.start". That was making some problems in DEXSeq, but I adapted 
>> the DEXSeq code to it. Could you try to update to the last version of 
>> the svn (1.3.16)?
>> Best wishes,
>> Alejandro
>> ps. I added copy to the Bioconductor mailing list in case someone is 
>> interested, could be helpful for people having the same error message
>>> Dear Alejandro,
>>> some time ago you helped me to solve a problem with
>>> estimateDispersions() in the DEXSeq package. I had to interrupt working
>>> on these data, but now I picked it up again and there seems to be
>>> another problem. This time estimateDispersins does not generate any
>>> results (as fa as I can tell), but without an error message. I attached
>>> my example data, the script and the messages to this mail. It would
>>> extremely nice of you, if you could have a look into it and give me a
>>> hint about what is going on.
>>> Best wishes,
>>> Georg

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