results from EMMAX software

Question

[hosin]

Hi there, I am using EMMAX software for an association analysis, as described in the manual , each line consist of 4 : SNP ID, Beta, SE(beta) and p-value in the output file (.ps file). But I just received 3 column ( I think just SNP ID, SE(beta) and p-value) in the out put like below:

SNP1    -0.100215783    0.23095596
SNP2    -0.154472206    0.050492626
SNP3    -0.06535533 0.537008626
SNP4    -0.041412454    0.611070227
SNP5    -0.167001348    0.013342496
SNP6    -0.005730355    0.958920667
SNP7    0.148709792 0.057797328
SNP8    -0.214196023    0.005016772

Is that right? I would be grateful if there are more experiences, or advises about this result

Answer 1

[Zhitian Wu]

You can download Intel compiled version of emmax on this page, and you'll get 4 columns then.

In your result, the 3rd column is p-value.

Anyway, I am not sure whether the result (p-value) differs between two versions of emmax.

[hosin]

Alright. Thank you very much