Post by Asling_GCTA on Jul 30, 2014 8:39:02 GMT
Hello,
I use GCTA to estimate the variance explained by GRM from a subset of snps for a binary trait. (0/1).Here is the reml result:
Source Variance SE
V(G) 0.003794 0.003079
V(e) 0.132379 0.003814
Vp 0.136173 0.002400
V(G)/Vp 0.027865 0.022593
The estimate of variance explained on the observed scale is transformed to that on the underlying scale:
(Proportion of cases in the sample = 0.174438; User-specified disease prevalence = 0.130000)
V(G)/Vp_L 0.055307 0.044844
logL 3190.744
logL0 3189.958
LRT 1.573
df 1
Pval 0.1049
n 6455
It seems that although GCTA gave the estimated variances on the liability scale, the Pvalue of LRT is not significant. So my question is that does this mean that the estimate itself is not valid?
Thank you!
Asling
I use GCTA to estimate the variance explained by GRM from a subset of snps for a binary trait. (0/1).Here is the reml result:
Source Variance SE
V(G) 0.003794 0.003079
V(e) 0.132379 0.003814
Vp 0.136173 0.002400
V(G)/Vp 0.027865 0.022593
The estimate of variance explained on the observed scale is transformed to that on the underlying scale:
(Proportion of cases in the sample = 0.174438; User-specified disease prevalence = 0.130000)
V(G)/Vp_L 0.055307 0.044844
logL 3190.744
logL0 3189.958
LRT 1.573
df 1
Pval 0.1049
n 6455
It seems that although GCTA gave the estimated variances on the liability scale, the Pvalue of LRT is not significant. So my question is that does this mean that the estimate itself is not valid?
Thank you!
Asling
