Question: topGO error with uniprot ID's
0
gravatar for MH
23 months ago by
MH0
MH0 wrote:

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

topgouniprot topgo R • 770 views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 23 months ago by MH0

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

ADD REPLYlink written 23 months ago by Kevin Blighe56k

Thanks for the feedback.

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

Mahmoud

ADD REPLYlink written 22 months ago by MH0
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