I am trying to run topGO but
new("topGOdata",
relatively frequently produces this kind of errors for some
selectedSet and backgroundSet.
MF ontology
Building most specific GOs .....
ontology: MF colnames Entry GO CC BP MF PE
( 725 GO terms found. )
Build GO DAG topology ..........
There are no adj nodes for node: GO:1904713
Show Traceback
Rerun with Debug
Can it have anything to do with the fact that I am using uniprot id -
goterm mappings downloaded from uniprot and that uniprot ships with
more goterms than those topGO knows about?
I have my own topGO compatible annFun.uniprot and I think my
functions works OK. I think so because new("topGOdata",
works for mice (mus musculus) most of the time but frequently fails for human.
Just wondering what I can do about it?
If anyone is interested in reproducing the errors plaese do feel free to install
https://github.com/wolski/topGOUniProt
devtools::install_github
and run the (failing examples) in topGODataNew which is facade to
topGO::new("topGOdata"
regards
Witold
--
Witold Eryk Wolski
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