Effective sample size in weighted-z meta-analysis

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Wenbin Mei

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Nov 5, 2025, 3:40:51 PM (6 days ago) Nov 5
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Hi plink team,
Thank you for providing such as nice tool! In https://www.cog-genomics.org/plink/1.9/postproc you mentioned "if the numbers of cases and controls are unequal, effective sample size should be 4 / (1/<# of cases> + 1/<# of controls>).". But some papers suggest Neff = 2 / (1/<# of cases> + 1/<# of controls>) (https://www.nature.com/articles/nprot.2014.071)
Shall we use 4 / (1/<# of cases> + 1/<# of controls>) or 2 / (1/<# of cases> + 1/<# of controls>) to calculate Neff?
Thanks



Chris Chang

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Nov 6, 2025, 12:20:53 AM (6 days ago) Nov 6
to Wenbin Mei, plink2-users
Work out what happens when the number of cases is equal to the number of controls.

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