topGO error with uniprot ID's

Question

[MH]

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

[Kevin Blighe]

Yes, this has been reported elsewhere with no clear solution. Here are some other places where it has been reported:

• https://support.bioconductor.org/p/91338/
• https://stat.ethz.ch/pipermail/bioconductor/2010-December/036720.html
• https://stackoverflow.com/questions/50016821/topgo-error-with-uniprot-ids

For fear that your question may go unanswered here, too, I suggest that you contact the developers of the topGOUniProt package

Kevin

[MH]

Thanks for the feedback.

I did contact them on github with no answer so far.

Mahmoud