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Why the polygenic risk scores calculated by Plink and PRSice-2 are different

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!

enter image description here

Plink formula enter image description here PRSice-2 formula

prs plink
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updated by Sam Sam • written by Phylicia • Phylicia

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.

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written by Sam Sam

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