Hi everyone,

I have trouble creating topGO object using my own data. Wondering if someone can help me with this!

I'm following a couple of tutorials and steps mentioned in the original ViSEAGO paper. Here are chunks from the tutorial and their links.

From the publication: ViSEAGO offers all statistical tests and algorithms developed in the Bioconductor topGO R package, taking into account the topology of GO graph by using ViSEAGO::create_topGO- data method followed by the topGO::runTestmethod.

Under 'Functional GO enrichment' in the tutorial, the following piece of code is used to generate the topGO object.

# create topGOdata for BP
BP<-ViSEAGO::create_topGOdata(
    geneSel=selection,
    allGenes=background,
    gene2GO=myGENE2GO, 
    ont="BP",
    nodeSize=5
)

I also referred to topGO's tutorial to make sure my data types are correct. Yet, there are some errors, that I have trouble dealing with.

For my data, I have the following code.

> ##################
> # create topGOdata for BP
> BP<-ViSEAGO::create_topGOdata(
+   geneSel=geneList_g1,
+   allGenes=topDiffGenes(geneList_g1),
+   gene2GO=myGENE2GO, 
+   ont="BP",
+   nodeSize=5
+ )

#error message:
allGenes contain genes redondancy.
duplicate elements were removed.
Error in .local(.Object, ...) : allGenes must be a factor with 2 levels

In my case, geneList_g1 is a named num with gene symbols and p-values (length 23 differentially expressed genes). This list already has genes with p<0.01, but even otherwise, this line gives the same error.

Using another command to creat topGO object, I get the following error.

> mysampleGOdata <- new("topGOdata",
+                     description = "my Simple session",
+                     ontology = "BP",
+                     allGenes = geneList_g1,
+                     geneSel = topDiffGenes,
+                     nodeSize = 1,
+                     annot = annFUN.db,
+                     affyLib = affyLib)

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

Build GO DAG topology ..........
    ( 0 GO terms and 0 relations. )
Error in if is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  : 
  missing value where TRUE/FALSE needed

Any help is much appreciated!! Thanks in advance! :)