On the problem of inflation in TWAS
Does TWAS yield inflated p-values?
Does TWAS yield inflated p-values?
Comments
(I have no idea.)
TWAS yields inflated p-values when the target trait is polygenic
Yes
See example in figure 1, pink area is much larger than the negligible blue area in this example
No, it’s not the prediction error
See figure Eχ2 does not depend on the precision consistent with established error in variable literature
It’s the polygenicity of Y since Eχ2 = 1 + N h2 Φ. The inflation is 0 when the polygenic component of Y = 0
Quite well
Yes
See inflation in figure when using UK Biobank genotype data and null traits Y. It will continue growing as N grows.