What causes highly inflated p values of X chromosome in PLINK association analysis?
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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optimistsso4co3 •
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