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! :)