Hi, I have calculated polygenic risk score by Plink and PRSice-2 and the results are consistent, but slightly different.
I traced the formulas of the two calculation methods, and they are almost the same except the ploidy part. But if ploidy is 2, the results will have a huge difference.
I have not searched the specific calculation ways of the two. Could you suggest what are the differences between the two calculation methods? Thanks!
Plink formula PRSice-2 formula