Hi,I have conducted GWAS with binary traits. From Q-Qplot I find my data should carry out correction for population structure. however, after two different methods (GC and EIGENSTRAT),Q-Qplots seem to be ok, the lambdas both are larger than 1.11 which are still beyond acceptable. Is the proper value of lambda essential?
Moreover, when I use plink for GC, the result line upper the red line(standard) on the QQplot would be adjusted to below the red line.When I use GenABEL the adjusted result will be better. I don't understand if the problem is with my original data or something else.
Thank you for any help.