Hi, I am trying to do an enrichment analysis with topGO and it gives results with zero significance as well as p-value, I don't understand why it happened. Please let me know if anyone knows anything regarding this script https://github.com/UPOBioinfo/sma3s/blob/master/script_enrichment_Sma3s_v2.R

library(topGO)
library(ALL)
file_genes <- "core_protein.csv"
Nodes <- 40
file_t <- "new.tsv"
genes <-read.csv(file_genes, header = F)$V1
head(genes)
GOesByID <-readMappings(file = file_t)
head(GOesByID)
bg_genes <-names(GOesByID)
compared_genes <-factor(as.integer(bg_genes %in% genes))
names(compared_genes) <-bg_genes
head(compared_genes)
GOdata <- new("topGOdata", ontology = "BP", allGenes = compared_genes,
            annot = annFUN.gene2GO, gene2GO = GOesByID)
#run fisher test
resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")

> resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher",pvalueCutoff = 0.05)

-- Classic Algorithm --
the algorithm is scoring 0 nontrivial nodes parameters: test statistic: fisher Warning message: In .local(object, test.stat, ...) :

No enrichment can pe performed - there are no feasible GO terms!**

I am not expert of R but i am trying to understand.. please excuse me if it is a silly question...

Thank you!

Feasible genes are those genes that have a GO mapping (e.g., there are GO terms that describe the gene). If none of your genes has a GO mapping, then it's impossible to do a GO analysis. You should check to see that the GOesByID is formatted correctly, and that the significant genes have mappings based on that object.