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5.9 years ago
MH
•
0
Hello everyone,
I have been trying to use topGO with uniprot IDs but unfortunately I have been stopped by this error:
There are no adj nodes for node: GO:0072661
Show Traceback
Rerun with Debug
Error in switch(type, isa = 0, partof = 1, -1) :
EXPR must be a length 1 vector
I even tried the code suggested as an example from package 'TopGoUniProt' with the same error:
library(topGOUniProt)
tmp <-uniprotTable2ProteinGOTable(ontology="CC",mapping=getMouseData(PE=1))
head(tmp)
protID <- unique(tmp[,1])
protIDbackground <- unique(tmp[1:200,1])
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1), ontology="BP" )
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1) , ontology="MF")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1) , ontology="CC")
tmp <- getHumanData(PE=1)
head(tmp)
protIDbackground <- unique(tmp[,"Entry"])
length(protIDbackground)
protID <- protIDbackground[1:100]
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=1) , ontology="BP")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=0) , ontology="MF")
res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getHumanData(PE=0) , ontology="CC")
summary(res)
This error has been reported by other users of topGO when using other annotation package but with no solution. Could you help on this issue please?
Thanks in advance,
MH
Yes, this has been reported elsewhere with no clear solution. Here are some other places where it has been reported:
For fear that your question may go unanswered here, too, I suggest that you contact the developers of the topGOUniProt package
Kevin
Thanks for the feedback.
I did contact them on github with no answer so far.
Mahmoud