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Question: goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
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gravatar for Bohdan Khomtchouk
21 months ago by
Stanford University
Bohdan Khomtchouk10 wrote:

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?

ADD COMMENTlink modified 21 months ago • written 21 months ago by Bohdan Khomtchouk10
1

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 4608

The warning is related to the pcls function in the mgcv package, which is to do with the calculations afterwards, not finding the gene lengths.

ADD REPLYlink modified 21 months ago • written 21 months ago by Mike Smith2.1k

Did you install the annotation package?

ADD REPLYlink written 21 months ago by b.nota290
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