goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
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7.0 years ago

Has anyone else encountered any issues with using mm10 in the goseq R package:

> pwf <- nullp(genes, "mm10", "geneSymbol")
Can't find mm10/geneSymbol length data in genLenDataBase...
Found the annotaion package, TxDb.Mmusculus.UCSC.mm10.knownGene
Trying to get the gene lengths from it.
Warning message:
In pcls(G) : initial point very close to some inequality constraints

mm9 works absolutely fine with geneSymbol but mm10 does not. Is this a bug?

RNA-Seq gene-ontology • 2.9k views
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Few pointers in the direction, people reporting same error.

GOSeq analysis problem with geneLenDataBase

mm10 goseq supported genome

plus the cross post https://support.bioconductor.org/p/77605/

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