Only positive enrichment score in GSEA

Question

[enee]

Hi everyone, I am a novice in the enrichment analyses and I have a problem with the gseGO function of the clusterprofiler package in R. Basically I'm analyzing mouse expression data and when I go to run the analysis with my code there seem to be only enriched pathways (with positive NES). I don't understand why if I use the human annotation org.Hs.eg.db my results and graphs come out as I expect them to. The first plot comes from the following code with mouse annotation (org.Mm.eg.db) and the second plot comes from the code with the human annotation.

GO_gsea <- function(df) { library(clusterProfiler) library(org.Mm.eg.db) geneList = df[,2] names(geneList) = as.character(df[,7]) geneList = sort(geneList, decreasing = TRUE) data_GO_GSEA <- gseGO(geneList = geneList, OrgDb = org.Mm.eg.db, ont = "BP", minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, keyType = "SYMBOL", pAdjustMethod = "BH", eps = 0) }
CeO2vsDiff1_gsea <- GO_gsea(CeO2vsDiff1) 
dotplot(CeO2vsDiff1_gsea, showCategory=10, split=".sign") + facet_grid(.~.sign)