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,
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?