Post by clement on Apr 2, 2014 16:27:25 GMT
Hello Jian,
I adjusted my outcome variable by age, sex, and covariates other than PCs. Then I ran GCTA with PCs as qcovar.
I got the following output:
Source Variance SE
V(G) 0.989846 0.452480
V(e) 0.000001 0.444583
Vp 0.989847 0.055956
V(G)/Vp 0.999999 0.449143
logL -313.036
logL0 -316.718
LRT 7.364
df 1
Pval 0.003
n 632
Is it safe to say that a significant portion of the variance in the score is explained by the SNPs in the GWAS, but the sample size is too small to get a precise estimate?
Also, the V(G)/Vp is 0.999999 whenever I included age/sex/etc (either by adjusting the score before running GCTA or including them as covariates during GCTA).
Thank you.
Clement
I adjusted my outcome variable by age, sex, and covariates other than PCs. Then I ran GCTA with PCs as qcovar.
I got the following output:
Source Variance SE
V(G) 0.989846 0.452480
V(e) 0.000001 0.444583
Vp 0.989847 0.055956
V(G)/Vp 0.999999 0.449143
logL -313.036
logL0 -316.718
LRT 7.364
df 1
Pval 0.003
n 632
Is it safe to say that a significant portion of the variance in the score is explained by the SNPs in the GWAS, but the sample size is too small to get a precise estimate?
Also, the V(G)/Vp is 0.999999 whenever I included age/sex/etc (either by adjusting the score before running GCTA or including them as covariates during GCTA).
Thank you.
Clement
