Normalized enrichment Score (NES) cut-off

Question

[shakyaram079]

One of my friends did GSEA and used NES cut-off value of equal or greater than 2 for upregulated gene sets. The cut-off value is arbitrary. He further did GO analysis of the enriched upregulated gene sets and got good results.

1. What would be the possible reasons for taking NES cut-off value of equal or greater than 2 for upregulated gene sets?

2. Why can't a cut-off value of 1.9 or 2.1 be considered?

3. Is there any research paper where the author used the same cut-off value 2?

Answer 1

[ATpoint]

The cut-off value is arbitrary.

Correct. So is p < 0.05.

What would be the possible reasons for taking NES cut-off value of equal or greater than 2 for upregulated gene sets?

None, it's arbitrary. Or ask this friend of yours.

Why can't a cut-off value of 1.9 or 2.1 be considered?

It's fine, but people like even numbers. Maybe ancient greeks did not, that's why we run 42.195 km in marathon instead of 42km.

Is there any research paper where the author used the same cut-off value 2?

I guess if you search PubMed long enough there is a reference for any wonky cutoff. Not that this makes it more robust.