--adap-permp not for multiple testing correction#4
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Conxz wants to merge 1 commit intoeskederks:gtex_v8from
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--adap-permp not for multiple testing correction#4Conxz wants to merge 1 commit intoeskederks:gtex_v8from
Conxz wants to merge 1 commit intoeskederks:gtex_v8from
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--adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction.
Owner
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Thanks for your comment. We correct for multiple testing by adapting the significance threshold based on the number of tests performed (Number of genes across tissues). I see that our wording in the script was indeed confusing.
From: Xiangzhen Kong <notifications@github.com>
Sent: Tuesday, 28 January 2020 11:51 PM
To: eskederks/eMAGMA-tutorial <eMAGMA-tutorial@noreply.github.com>
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Subject: [eskederks/eMAGMA-tutorial] --adap-permp not for multiple testing correction (#4)
…--adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction.
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#4
Commit Summary
* --adap-permp not for multiple testing correction
File Changes
* M eMAGMA tutorial PART_1.md<https://github.com/eskederks/eMAGMA-tutorial/pull/4/files#diff-0> (2)
Patch Links:
* https://github.com/eskederks/eMAGMA-tutorial/pull/4.patch
* https://github.com/eskederks/eMAGMA-tutorial/pull/4.diff
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eskederks
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Jan 28, 2020
Author
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Great. That's clear now. I raised this because a student asked me about this issue after reading this eMAGMA tutorial. Permutation-based testing and permutation-based correction always make people confused. |
Owner
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Yes, I agree! I accepted your change, thanks again
From: Xiangzhen Kong <notifications@github.com>
Sent: Wednesday, 29 January 2020 10:46 PM
To: eskederks/eMAGMA-tutorial <eMAGMA-tutorial@noreply.github.com>
Cc: Eske Derks <Eske.Derks@qimrberghofer.edu.au>; Comment <comment@noreply.github.com>
Subject: Re: [eskederks/eMAGMA-tutorial] --adap-permp not for multiple testing correction (#4)
Great. That's clear now. I raised this because a student asked me about this issue after reading this eMAGMA tutorial. Permutation-based testing and permutation-based correction always make people confused.
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--adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction.