Question: topGO: "There are no adj nodes for node"
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gravatar for natske
3 months ago by
natske10
natske10 wrote:

Hi, I'm getting an error with some topGO code which used to work. The below code is an example, so you should be able to just paste it in:

library("org.Hs.eg.db")
library("topGO")
all_genes <- rep(c(0,1,1), each=10)
names(all_genes) <- c("LEF1","FOXJ2","ZNF654","TAL1","ZMYM2","DCAF6","PDP1","ZNF302","TMED4","SLC5A6","PLSCR1","RPL41","MARK1","TMSB10","HES6","CACNA2D3","PDLIM1","KLB", "MTMR3","LOC100506804","INPP4B","PSMD4","DPM2","DCAF5","PTPN1","POLE2","POU6F1","IL18R1","POU5F1","PITPNA")
GOdata <- new("topGOdata", ontology = "BP", allGenes = all_genes, geneSel = function(p) p == 1, description = "Test", annot = annFUN.org, mapping="org.Hs.eg.db", ID="Symbol")

 

The error message that I get is:

Building most specific GOs ..... ( 232 GO terms found. )

Build GO DAG topology ..........

There are no adj nodes for node: GO:0120163 Error in switch(type, isa = 0, partof = 1, -1) : EXPR must be a length 1 vector

Same error occurs if I use org.Mm.eg.db:

library("org.Ms.eg.db")
all_genes_ms = rep(c(0,1,1), each=10)[1:26]
names(all_genes_ms) = c("Zfp654","Foxj2", "Dcaf6", "Zmym2", "Klb","Dcaf5", "Pole2", "Inpp4b","Ptpn1", "Hes6",  "Slc5a6","Mtmr3", "Tal1",  "Il18r1","Pdp1",  "Plscr1","Mark1", "Tmed4", "Psmd4", "Pitpna","Cacna2d3","Pou6f1","Lef1","Pou5f1","Pdlim1","Dpm2")
GOdata <- new("topGOdata", ontology = "BP", allGenes = all_genes_ms, geneSel = function(p) p == 1, description = "Test", annot = annFUN.org, mapping="org.Mm.eg.db", ID="Symbol")

 

Would be great if anyone has any insight into what has gone wrong.

Thanks!

ADD COMMENTlink written 3 months ago by natske10

After restarting Rstudio, the error has vanished. Quite bizarre.

ADD REPLYlink modified 3 months ago • written 3 months ago by natske10
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