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Has anyone else encountered any issues with using mm10 in the goseq 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?
Is this really an error? It looks like it couldn't find the gene length in a the database, so it grabbed the TxDB and calculated them from there - which sounds sensible. If you try to find only the gene lengths using
getlength()does it work as expected? e.g.> getlength(c("MYC", "CDC6"), "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. [1] 2396 4608The warning is related to the
pclsfunction in themgcvpackage, which is to do with the calculations afterwards, not finding the gene lengths.Did you install the annotation package?