Question: goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
0
gravatar for Bohdan Khomtchouk
3.3 years ago by
Stanford University
Bohdan Khomtchouk320 wrote:

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 • 1.2k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Bohdan Khomtchouk320

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/

ADD REPLYlink written 3.3 years ago by Sukhdeep Singh9.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 635 users visited in the last hour