I've detected selection using different methods. let's talk about CLR method.
What I did is I selected positions that have 1% highest CLR value (high CLR values denote a candidate region for a selective sweep). and crossed the position with the annotation and I got 1200 genes.
Imagine that MYB transcription factor was in the list of candidate regions that are under selection.
There is probably several hundreds of MYB in the genome, so it's very likely that I can find them in the peaks by chance.
How would you really say this gene was under selection if it's at the end is a matter of chance?