I am doing SNP association study, and the estimated p-values for each SNP are plotted as a QQ-plot. The question is, can one interpret false positive hits from a QQ-plot in GWAS (Genome-Wide Association Study)?
From this article: http://www.genomesunzipped.org/2010/07/how-to-read-a-genome-wide-association-study.php , it says:
"...on the other hand, should show a solid line matching X=Y until it sharply curves at the end (representing the small number of true associations among thousands of unassociated SNPs)"
Is this always true, or may False Positive also deviate sharply at the end of the curve? How to tell from a QQ-plot if a deviation is because of a true association or a false association?