--adap-permp not for multiple testing correction

[Conxz]

--adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction.

[eskederks]

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 <[email protected]> Sent: Tuesday, 28 January 2020 11:51 PM To: eskederks/eMAGMA-tutorial <[email protected]> Cc: Subscribed <[email protected]> Subject: [eskederks/eMAGMA-tutorial] --adap-permp not for multiple testing correction (#4)

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--adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction.

________________________________ You can view, comment on, or merge this pull request online at: #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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#4?email_source=notifications&email_token=AKTD7YT5AUHSYYIALTRNPPLRAAZ45A5CNFSM4KMSYFV2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IJHJE6Q>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKTD7YTBLL2ALIGE3735XQDRAAZ45ANCNFSM4KMSYFVQ>.

[Conxz]

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.

[eskederks]

Yes, I agree! I accepted your change, thanks again From: Xiangzhen Kong <[email protected]> Sent: Wednesday, 29 January 2020 10:46 PM To: eskederks/eMAGMA-tutorial <[email protected]> Cc: Eske Derks <[email protected]>; Comment <[email protected]> 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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#4?email_source=notifications&email_token=AKTD7YWRS46NWFBV5WJJG2TRAF3AVA5CNFSM4KMSYFV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKHCBGI#issuecomment-579739801>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKTD7YT4A4WHKV2RPTYEOHLRAF3AVANCNFSM4KMSYFVQ>.