I am running an analysis of two phenotypes: mutant and control.

I have a statistic used to rank the different genes, and the ranking is exactly the opposite between mutant and control. Moreover, there are no duplicates in the ranking (which excludes that genes are ranked alphabetically). I uploaded the test file [here](https://pastebin.com/raw/JKEJ20xF).

My expectation is that running GSEA using mutant as positive phenotype, should give me the same results (but in opposite direction) than running GSEA using control as a positive phenotype - since there are only two phenotypes, and the ranking statistic is computed mutant vs control.

However, when I run Gene Set Enrichment Analysis using mutant as positive phenotype, the results I get are not the same with respect to running GSEA using mutant as negative phenotype.

I initially thought that it might be related to the choice of the random seed, however, I get the same results even setting the same random seed in all runs.

The following is an example of an enriched result of the positive phenotype:

[![enter image description here](https://i.stack.imgur.com/ATA63.png)](https://i.stack.imgur.com/ATA63.png)

[![enter image description here](https://i.stack.imgur.com/1pBeX.png)](https://i.stack.imgur.com/1pBeX.png)

The same results with the negative phenotype:

[![enter image description here](https://i.stack.imgur.com/ZNitu.png)](https://i.stack.imgur.com/ZNitu.png)
[![enter image description here](https://i.stack.imgur.com/dnGFo.png)](https://i.stack.imgur.com/dnGFo.png)

The ranking is exactly the same, however, the leading edge is different in the two cases. It's probably due to the fact that the ranking sum goes in one direction (increasing the enrichment score) in both phenotypes. This is probably the cause of different scores in the opposite phenotypes, however, which is the result I should use in this case?