I am getting interested in R/Bioconductor packages and trying to learn about it. I want to perform HyperGeometric test for over representation against GO and KEGG. I have go two text files: Back.txt and genes.txt. To test HyperGeometric test I wrote following code in R. The result with be in data.frame and visualizing in the Gograph or KEGG pathway.
library(topGO) library(GOstats) universe=read.table("Back.txt", sep=",") # Background files where only entrez id's are listed without heading column tbl <- read.table ("genes.txt", sep=",") # selected genes with following header Probes_id,entrez_gene_id,symbols,P.Value and F.C selected=<-tbl$V2 # Selecting only second column of tbl vector where entrez_gene_id is present param <- new ("GOHyperGParams", geneIds = selected, universeGeneIds=universe, annotation="org.Hs.eg.db", ontology="BP",pvalueCutoff=0.1, conditional=FALSE,testDirection="over")
But, I couldn't succeeed because I get the error
Error in makeValidParams(.Object) : geneIds and universeGeneIds must have the same mode geneIds: NULL universeGeneIds: integerFALSE In addition: Warning message: In makeValidParams(.Object) : converting univ from list to atomic vector via unlist
hyp <- hyperGTest (param)
Error in is(object, Cl) : error in evaluating the argument 'p' in selecting a method for function 'hyperGTest'
Am I missing something here? Do I have to go through more resources to clear my understanding? if yes where can I find R/Bioconductor HyperGeometric test with all needed R packages?
Plus I have loaded all the library and packages, shown in the link ( http://pastebin.com/i735EUWp )