Entering edit mode
9.3 years ago
summeryhx
•
0
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?
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).