Entering edit mode
8.2 years ago
Bohdan Khomtchouk
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350
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?
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/