Corrected lambda is large

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Joined: Thu Oct 09, 2014 2:43 am

Corrected lambda is large

Postby snowy » Sat Oct 11, 2014 2:10 am


I have conducted GWAS with binary traits, and after the process qtscore(),got a lambda of 1.31,then I tried to correct it for
population structure with all the three methods (PCBA,GC,EIGENSTRAT).But the corrected lambdas are still lagre (>1.1),
especially to be 1.46 after GC and EIGENSTRAT.I don't understand if the problem is with my original data or something else.

At the beginning I used C1~C5 as the PCs to correct,and the lambda is 1.12. When I adjusted th PCs from C1 to C7,
lambda dropped to 1.07. I'm not sure whether the result is reliable.

I would be really grateful if anyone could provide some explanations for that.

Thank you.

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