Hi, 

I am trying to create the topGOdata object with the following command, 

sampleGOdata <- new("topGOdata", description = "IFNa",
                    ontology = "BP",
                    allGenes = Vector_data, 
                    geneSel = topDiffGenes, 
                    nodeSize = 10,
                    annot = annFUN.org, 
                    mapping="org.Hs.eg.db",
                    ID = "Entrez"
                    )

Where Vector_data contains my Entrez ID with its fold change

And my topDiffGenes function defined as Fold change > 2

I get the error:

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

Could anyone help me with this?