[Bioc-devel] topGO - BPontology Building most specific GOs ..... ontology: BP colnames Entry GO CC BP MF PE ( 2631 GO terms found. ) Build GO DAG topology .......... There are no adj nodes for node: GO:1904722

[Witold E Wolski]

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