qqplot result of the gwas
I'm doing a gwas with 200+samples and get the qqplot with the P-value of the logistic analysis include the PCs and age as the covariates, However, the qqplot is weird , is show a solid line matching X=Y until it sharply curves at the end ,not upper the line(x=y),but under it.
Anyone could help me out the problem? Is that because there are no true associations among SNPs? or is there something wrong in my analysis?
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summeryhx •
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Can you post the figure with labeled axes? We can only assume your x is expected vs y is observed, but in either case, the top right would be p=1.0, indicating non-significant points. a divergence here indicates distributional problems from the statistical assumption, but it doesn't mean anything to your signal in the lower left. (unless you're plotting minus log P, and I have it backwards).