Doubts of S PrediXcan phi inflation correction

[juditcd]

Dear developers,

Thank you very much for such an amazing tool and for the continuous improvements you have made to it.

I have a question regarding the phi inflation correction. When working with case–control samples, would it be more appropriate to use the effective sample size (Neff) or the total sample size (N)? Additionally, for SNP-based heritability, should the estimates be reported on the observed scale or on the liability scale?

Best regards,

Judit

[hakyim]

Hi Judit, this is a great question and one that we haven't explored. We would need to run some simulations and check what would be the best approach. I would try with Neff and total sample size and see what the results look like. But again, this is something that needs to be explored. Similarly for the observed vs liability scale heritability. Haky

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On Wed, Sep 17, 2025 at 7:36 AM juditcd ***@***.***> wrote: *juditcd* created an issue (hakyimlab/MetaXcan#219) <#219> Dear developers, Thank you very much for such an amazing tool and for the continuous improvements you have made to it. I have a question regarding the phi inflation correction. When working with case–control samples, would it be more appropriate to use the effective sample size (Neff) or the total sample size (N)? Additionally, for SNP-based heritability, should the estimates be reported on the observed scale or on the liability scale? Best regards, Judit — Reply to this email directly, view it on GitHub <#219>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAW2ROL7MJF2DO3NLJXDZS33TFIWRAVCNFSM6AAAAACGYD2LF2VHI2DSMVQWIX3LMV43ASLTON2WKOZTGQZDMMJRG4YDMMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>