What causes highly inflated p values of X chromosome in PLINK association analysis?
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Entering edit mode
2.0 years ago

I get ~5% positive rate in all chromosomes, yet X has 13% positivity rate. What could be causing that? I'm performing plink --logistic with --xchr-model 2.

Edit: I replicated analysis separate for each sex and in males inflation disappears, while in females it prevails exactly as high.

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