Help with CummeRbund error.. I'm lost

beeman · 08-31-2014, 06:54 PM

Hi,

I am trying to use cummeRbund to process cuffdiff output, but I'm getting an error message that I'm not sure how to solve.
-------------------
Slots:
annotation
fpkm
repFpkm
diff
count
isoforms CuffFeatureSet instance of size 132
TSS CuffFeatureSet instance of size 72
CDS CuffFeatureSet instance of size 49
promoters CuffFeatureSet instance of size 38
splicing CuffFeatureSet instance of size 72
relCDS CuffFeatureSet instance of size 38
character(0)
[1] 0
No gene set returned (Gene might not be in database?)
Error in validObject(.Object) : invalid class CuffGene
Calls: getGene ... callNextMethod -> eval -> eval -> .nextMethod -> validObject
Execution halted

---------------------

Has anyone run into this problem before and can suggest a fix or at least where the problem may lie?? :/

Thanks

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08-31-2014, 06:54 PM	#1
beeman Member Location: Australia Join Date: May 2012 Posts: 20	Help with CummeRbund error.. I'm lost Hi, I am trying to use cummeRbund to process cuffdiff output, but I'm getting an error message that I'm not sure how to solve. ------------------- Slots: annotation fpkm repFpkm diff count isoforms CuffFeatureSet instance of size 132 TSS CuffFeatureSet instance of size 72 CDS CuffFeatureSet instance of size 49 promoters CuffFeatureSet instance of size 38 splicing CuffFeatureSet instance of size 72 relCDS CuffFeatureSet instance of size 38 character(0) [1] 0 No gene set returned (Gene might not be in database?) Error in validObject(.Object) : invalid class CuffGene Calls: getGene ... callNextMethod -> eval -> eval -> .nextMethod -> validObject Execution halted --------------------- Has anyone run into this problem before and can suggest a fix or at least where the problem may lie?? :/ Thanks