Question: qqplot for the P-values dervided from permutation test in Plink
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gravatar for Shicheng Guo
2.3 years ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Any one tried qq-plot for the P-values derived from permutation test in plink (Both EMP1 and EMP2)?

I get a quite strange qq-plot for the pvalues from permutation test to linear regression (phen ~ geno + age)

I also want to know the relationship between EMP1 and EMP2.

EMP1 > EMP2 or EMP1 < EMP2 or they don't have any relationship?

Thanks.

Here, I give a qq-plot for linear regression (phen ~ geno + age)

enter image description here

qqplot plink permutation • 1.6k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Shicheng Guo8.3k
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Please share the QQ plots via, for example, ImgB. How about the non-permuted P values? How have you pre-filtered your SNPs? - genomewide or focused on a particular locus?

Also to add: if you have low sample numbers or your cases/controls are unbalanced, then QQ plots will invariably look odd, or, if you are adjusting too much, they may also look odd.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Kevin Blighe61k
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You edited the post, I see - thanks!

EMP1 is the empirical P value whilst EMP2 is the correct P value (after permutation). Your QQ plot for EMP2 looks 'fine'. My thoughts are that the small tail at the top-right of the EMP2 QQ plot may be SNPs that are related to your phenotype of interest (phen).

If the P values fit perfectly to the expected distribution, then, of course, it would indicate that your populations indicated by phen are the same (null hypothesis).

ADD REPLYlink written 2.3 years ago by Kevin Blighe61k
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Hi Kevin, It's genome-wide association P-values, not selected from any chrosome. The top-right of EMP2 is my interesting SNPs. But 1) I don't understand EMP1, why they are lower in expected quantiles of P-values 2) I don't understand the relationship between EMP1 and EMP2.

Also I don't understand is that for some SNPs, the P-values of EMP2 is smaller than EMP1

ADD REPLYlink written 2.3 years ago by Shicheng Guo8.3k
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Yes. Chris told me these EMP1 and EMP2 is only for genetics variants, not for covariants. If I want to show the P-values for co variants I can add --tests

ADD REPLYlink written 2.3 years ago by Shicheng Guo8.3k
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Hi Kevin, How to understand the observed P-value in left figure is lower than the expectation regions? and sometimes, the observed P-values in higher than expected regions (null hypothesis). Which factors will caused the observed P-value higher or lower than the expected regions (grey region in the figure) . Thanks.

ADD REPLYlink written 2.2 years ago by Shicheng Guo8.3k

To help to understand that, you may want to take a look at this Stats StakOverflow answer: https://stats.stackexchange.com/questions/101274/how-to-interpret-a-qq-plot

  • Above the expected distribution implies that the data is more 'spread' (dispersed) than expected.
  • Below the expected distribution implies that the data is more 'compressed' than expected
ADD REPLYlink written 2.2 years ago by Kevin Blighe61k
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