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3 months ago

Phylicia
▴
10

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

The equation of PRSice and PLINK is actually the same. Unless you have more information e.g. PRSice version number, you data information, threshold used etc, I won't be able to answer your question.