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3 hours ago by

Gene adj.P.Val
ENSDARG00000087345 1.39E-128
ENSDARG00000058371 5.68E-50
ENSDARG00000026403 1.77E-48
ENSDARG00000006427 2.36E-48
ENSDARG00000041381 8.10E-39
ENSDARG00000071601 1.81E-33
ENSDARG00000054191 2.73E-32
ENSDARG00000098488 5.67E-31
ENSDARG00000076129 2.31E-29
ENSDARG00000035438 7.14E-28
ENSDARG00000010155 1.26E-27
ENSDARG00000090039 2.57E-27
ENSDARG00000061547 1.17E-25
ENSDARG00000035835 1.32E-23
ENSDARG00000103760 2.10E-23.

It has been loaded into the data frame like

tmp <- read.delim("E:/ensembl_example_input.txt")

I am trying to do top GO annotation using the topGo project.

The code snippets Iam following are

geneList <- tmp$adj.P.Val
names(geneList) <- tmp$Gene
# Create topGOData object
GOdata <- new("topGOdata",
    ontology = "BP",
    allGenes = geneList,
    geneSelectionFun = function(x)x,
    annot =, mapping = ""). The error I am getting is as follows
Building most specific GOs .....
    ( 0 GO terms found. )

Build GO DAG topology ..........
    ( 0 GO terms and 0 relations. )
Nothing to do:
Error in split.default(names(sort(nl)), f.index) : 
  first argument must be a vector.


modified 14 minutes ago

3 hours ago


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