inflated QQ-PLOT


Dear All,

I did linear regression in plink/1.90 for quantitative trait (N=450) using SNP array data. Plotted qq plot using QQ-man package in R. I got the following qq plot which shows a sharp peak followed by downward trend; i am confused why the downward trend after the peak; Any possible explanations would be highly appreciated. Regression adjusted for PC1-PC5, and 3 clinical covariates.

Thanks in advance ! (I am new to field of genetics)

qq plot






The p-values can be regarded as right-skewed, I guess, heavily-skewed, with that well-defined 'tail' that wanders up from x = 3. The other points that are then at the same value of y at the end of this tail are indicative of p-values that are the same. This could occur via over-adjustment via the 5 PCs + 3 covariates. Do you need 5 PCs and have evidence that they are important?

For example, if I look at this, I'd be happy to just have PC1 and PC3 as covariates:

[from Produce PCA bi-plot for 1000 Genomes Phase III - Version 2]

Similar question for the other covariates, and also are these logged or set to some power?

Sample size? selection criteria? QC of data?

Various things to consider.


before adding your answer.

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