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I wonder if there's a way to calculate the combined odds ratio for certain SNPs in a meta-analysis of a several GWAS, even when you don't have the SE, neither beta, for each individual study?

Thank you!

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    $\begingroup$ Do you have the confidence interval? SE can be back calculated from that. Also, you say that you don't have the betas, but I suppose that you have the OR's. In that case the betas can be calculated by taking the natural logarithm of the OR's. $\endgroup$
    – boscovich
    Mar 17, 2012 at 8:34
  • $\begingroup$ ...or the p-values? If you have precise p-values you can back-calculate SEs from them. $\endgroup$
    – onestop
    Mar 17, 2012 at 8:56

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It sounds like you only have p-values for each SNP. In this case you can use Fisher's method, but it is a rather crude analysis. Not only will meta-analyzing betas and SEs give you better power, but it also permits estimation of an overall effect, which will be useful in many ways, not least planning replication studies.

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