I am working with a non-model fungus and trying to do gene enrichment analysis for differentially expressed genes. For this I got the GO terms for a list of genes using InterProscan. Now I am using these list of genes with respective GO terms to do enrichment analysis and to make plots in R using TopGO package.
I am following thisworkshop from UCdavis to achieve my goal, however I have a small problem with the p-value. I used this code to list the gene with the p-values
tmp <- ifelse(DE$adj.P.Val < pcutoff, 1, 0) geneList <- tmp
and I am getting the following final result:
GO.ID Term Annotated Significant 1 GO:0008213 protein alkylation 1 1 2 GO:0046903 secretion 1 1 3 GO:0042219 cellular modified amino acid catabolic process 1 1 4 GO:0006979 response to oxidative stress 1 1 5 GO:0019438 aromatic compound biosynthetic process 77 77 6 GO:0015672 monovalent inorganic cation transport 2 2 Expected raw.p.value 1 1 1 2 1 1 3 1 1 4 1 1 5 77 1 6 2 1
Instead of raw.p.value as 1 I need the actual p-values I provided in the file. Can you please help, if I am missing anything. I went over my codes multiple times but I have not done anything different as mentioned in the tutorial but my results are different from what I need.
I will appreciate your help. Thanks, Ambika