Whenever you perform an XP-EHH analysis involving populations, you tend to perform many pairwise XP-EHH calculations. During those scenarios, what is the best way to detect outliers? Currently, for all pairwise comparison, the XP-EHH scores were calculated per chromosome. the scores were converted to z-scores which were then converted to absolute Z-score. All the chromosomes were joined to get the whole genome XP-EHH plot.
What is the correct way to assign a threshold to detect outliers?