top geo ontology
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6 weeks ago
aranyak111 • 0

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 = annFUN.org, mapping = "org.Dr.eg.db"). 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.
RNA-Seq • 256 views
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The column names in your sample data and code don't match. Also, invest a bit more time formatting your post better.

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And it looks like you re-edited your post to remove the code formatting that I added - please re-format it better.

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Hello aranyak111!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/15492/

This is typically not recommended as it runs the risk of annoying people in both communities.

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