inflated QQ-PLOT

1

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


QQ-plot


inflation


GWAS


plink

• 92 views

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:
biplot-new

[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.

Kevin


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