There are no adj nodes for node:

[Mahmoudhallal]

Hello Wolski,

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 you suggested as an example 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

[nasiegel88]

I have this same error when I try to knit my markdown file. For some reason, the error does not occur when I run all my code chunks...weird