Question: Plink Permutation EMP1 & EMP2

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nbotha1994 •

**0**wrote:What is the difference between the two empirical p-values, EMP1 and EMP2, generated by permutation, using Plink?

The only description they give is the following: "two sets of empirical significance values can then be calculated -- pointwise estimates of an individual SNPs significance, but also a value that controls for that fact that thousands of other''

As far as I understand is that EMP1 is after a 1000 permutations and EMP2 is after adjusting for multiple testing. OR is EMP1 only after a proportion of permutations have been performed and EMP2 after the full 1000 permutations?

For a result of mine the EMP1 result is significant (p<0.05). However, the EMP2 is not - What does that mean?

Please help.

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modified 28 days ago
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Kevin Blighe ♦

**41k**• written 29 days ago by nbotha1994 •**0**
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