Post by katya on Jun 4, 2015 19:00:48 GMT
Dear all,
I am new to using GCTA and obtained a confusing result when trying to partition heritability by chr. The overall heritability is h2=0.31, se=.17, p=0.029. When I run REML for each chromsome separately, heritability for each chr equals to h2=0.31, se=.17, p=0.029:
Chr V(G)/Vp SE Pval
1 0.310149 0.167439 0.03035
2 0.310149 0.167439 0.03035
3 0.310149 0.167439 0.03035
...
22 0.310149 0.167439 0.03035
23 0.310149 0.167439 0.03035
However, when I run a join REML, all chromosomes except for chr2, have the following values h2=0.014, se=.000437, which would all sum up to 0.31:
V(G1)/Vp 0.014098 0.000437
V(G2)/Vp 0.000001 0.168501
V(G3)/Vp 0.014098 0.000437
V(G4)/Vp 0.014098 0.000437
V(G5)/Vp 0.014098 0.000437
...
What may be the issue here?
I am new to using GCTA and obtained a confusing result when trying to partition heritability by chr. The overall heritability is h2=0.31, se=.17, p=0.029. When I run REML for each chromsome separately, heritability for each chr equals to h2=0.31, se=.17, p=0.029:
Chr V(G)/Vp SE Pval
1 0.310149 0.167439 0.03035
2 0.310149 0.167439 0.03035
3 0.310149 0.167439 0.03035
...
22 0.310149 0.167439 0.03035
23 0.310149 0.167439 0.03035
However, when I run a join REML, all chromosomes except for chr2, have the following values h2=0.014, se=.000437, which would all sum up to 0.31:
V(G1)/Vp 0.014098 0.000437
V(G2)/Vp 0.000001 0.168501
V(G3)/Vp 0.014098 0.000437
V(G4)/Vp 0.014098 0.000437
V(G5)/Vp 0.014098 0.000437
...
What may be the issue here?
