topGO error: Building most specific GOs ..... ( 0 GO terms found. )

Question

[park.seojeong2]

Hi, guys. I have got an error using topGO. Could you check my scripts and say what is something wrong with me?

> coreGenes <- read.table("go_annotations.txt")`
>  head(coreGenes)

# MSTRG.10.1    GO:0003674,GO:0003824,GO:0004175,GO:0004190,GO:0005575
# MSTRG.100.1   GO:0000166,GO:0003674,GO:0003676,GO:0005488
# MSTRG.1004.1  GO:0003674,GO:0005488,GO:0005575,GO:0005576
# MSTRG.1006.1  GO:0003674,GO:0003676,GO:0003824,GO:0003964
# MSTRG.1007.1  GO:0003674,GO:0003824,GO:0004497,GO:0005488
# MSTRG.1008.1  GO:0003674,GO:0003824,GO:0004497,GO:0005488,GO:0005506

> geneID2GO <- readMappings("gene2go")
> str(head(geneID2GO))

#List of 6
# $ #tax_id: chr "GeneID"
# $ 3702   : chr "814629"
# $ 3702   : chr "814629"
# $ 3702   : chr "814630"
# $ 3702   : chr "814630"
# $ 3702   : chr "814630"

> geneNames <- names(geneID2GO)
> head(geneNames)

#[1] "#tax_id" "3702"    "3702"    "3702"    "3702"    "3702"   

> myInterestingGenes <- sample(geneNames, length(geneNames) / 10)
> geneList <- factor(as.integer(geneNames %in% myInterestingGenes))
> names(geneList) <- geneNames
> str(geneList)

# Factor w/ 2 levels "0","1": 1 2 2 2 2 2 2 2 2 2 ...
# - attr(*, "names")= chr [1:2161655] "#tax_id" "3702" "3702" "3702" ...

> GOdata <- new("topGOdata", ontology = "BP", allGenes = geneList,
              annot = annFUN.gene2GO, gene2GO = geneID2GO)

###########################
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

I have searched several websites to use topGO for non-model organisms and scripts worked!

However, that scripts do not work today.

Maybe something went wrong during the organization and save process of scripts.

What did I wrong?

Thank you in advance.

[Jean-Karim Heriche]

Check the manual/docs. I think that readMappings() is meant to read a custom annotation file, e.g. your file "go_annotations.txt". Currently your geneID2GO doesn't seem to contain any GO term. Also for enrichment analysis I think the topGOData object should contain two lists of genes.

[park.seojeong2]

Thank you for your rely! You mean I have to change data uploaded as geneID2GO first, aren't you? And you said "topGOData object should contain two lists of genes.". Does it means that i need to change scripts for topGOData to have two lists of gene? Could you show me an example? I'm not used to using r...

[Jean-Karim Heriche]

I haven't used topGO in a while so don't remember the details. However, Bioconductor packages are generally well documented. Check the topGO package vignette for examples.

[Ram]

Why did you delete the post, park.seojeong2 ?