GSEA gave exact same results for data ranked differently

MetaboAnalyst
1

Hi,

I have two datasets with the same set of features but with different rankings of the features. When I run GSEA, I got the exact same results for these two datasets. Below is how I run the analysis:

mSet<-InitDataObjects("mass_all", "mummichog", FALSE, 150)
mSet<-SetPeakFormat(mSet, "rmt")
mSet<-UpdateInstrumentParameters(mSet, 10.0, "mixed", "yes", 0.02);
mSet<-Read.PeakListData(mSet, "path_to_file");
mSet<-SanityCheckMummichogData(mSet)
mSet<-SetPeakEnrichMethod(mSet, "gsea", "v2")
mSet<-PerformPSEA(mSet, "zma_kegg", "current", 3 , 100)

I have attached the two datasets here.
MetaboAnalystInput_Root.csv (18.3 KB)
MetaboAnalystInput_Shoot.csv (18.3 KB)

Based on my understanding, if the features are ranked differently, GSEA shouldn’t yield the same results. I’d appreciate it if you could provide any help. Thank you!