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! :)