Change genome-wide P threshold to control FDR

[seanlzheng]

Thank you for developing and maintaining this excellent tool for the genomics community!

My understanding is that the computed maxFDR refers to the FDR at P 5E-8 threshold. If I am correct, is it possible to adjust the genome-wide P threshold to account for this e.g. calculate how much to reduce the P threshold by to control the FDR to a given %?

Thanks in advance

[paturley]

You are right. It's the maximum potential FDR given the Omega and Sigma matrices for a threshold of 5e-8.

That's a really interesting idea you have though, but not one that we incorporated into the MTAG software. To do this, you'd probably need to dig into the hardcoded thresholds of the MTAG software and make those changes.

On Wed, Dec 13, 2023 at 6:10 AM seanlzheng @.***> wrote:

Thank you for developing and maintaining this excellent tool for the genomics community!

My understanding is that the computed maxFDR refers to the FDR at P 5E-8 threshold. If I am correct, is it possible to adjust the genome-wide P threshold to account for this e.g. calculate how much to reduce the P threshold by to control the FDR to a given %?

Thanks in advance

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