[BioC] error in DEXSeq fitDispersionFunction()

Georg Otto gwo at well.ox.ac.uk
Wed Aug 8 12:37:00 CEST 2012

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?



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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