I have tried to perform enrichment analysis on reactome with a list of 481 genes. I have tried using reactomePA (R package), reactome website analysis tool, and enrichR (which has reactome2016 database) and I got different results:
ReactomePA: 843 terms
Reactome analysis tool: 1277 terms
Reactome 2016 enrichR: 788 terms
Since enrichR is older compare to the others, I am not surprised to have fewer terms but I don`t understand why comparison reactomePA and reactome analysis tool I got so different results. is it possible that I wrote a wrong script for reactomePA?
My dataset looks like:
# A tibble: 6 x 2 Entrezgene_ID log2fc <chr> <dbl> 1 14 -1.02 2 80755 -1.45 3 60496 -1.17 4 6059 -1.48 5 10061 -1.35 6 10006 -1.51
and my code for reactomePA is:
#load packages library(org.Hs.eg.db) #human genome library(DOSE) library(ReactomePA) # to perform enrichment analysis #organise the datasets genes <- d[] #numeric vector #selected log2fc names(genes) <- d[] #named vector geneLIST <- sort(genes, decreasing = TRUE) #decreasing order head(geneLIST) de <- names(geneLIST) head(de) x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T) head(as.data.frame(x)) x@result # 843 terms
Did I have done something wrong?
Thank you in advance