Meta analysis by plink

Question

[khn]

Hello all,

I am conducting meta-analysis by plink. I created two files, following the website of plink. The headers for the two files are CHR BP A1 A2 SNP BETA SE P. I ran --meta-analysis but the error message shows "no effect sizes are found". I just changed only the header from BETA to OR, and it worked. But now I need to convert the results of beta to odds ratio for meta-analysis.

But do I really need to convert BETA to OR as the plink does not read BETA? It seems that BETA can be the header per the website of plink. http://zzz.bwh.harvard.edu/plink/metaanal.shtml Do you have any experiences?

Thank you in advance.

Answer 1

[khn]

I think I figured out the answer - if we want to use BETA as a effect size, we must add +logscale in the code...