gravatar for Ambika

6 hours ago by

United States

Hello everyone,

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


modified 4 hours ago

6 hours ago


Source link