-
Notifications
You must be signed in to change notification settings - Fork 68
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Multiple Testing Correction in BUSTED vs absREL #1707
Comments
Dear @NicMAlexandre, There really isn’t anything formal that I ever wrote. Your specific application matters quite a bit. Not knowing anything else, I would recommend FDR for BUSTED. aBSREL is a bit more complicated, because it does multiple testing correction at the level of branches for each run. You can layer another correction on top of that if you want, probably another FDR. Can you give me any details? Best, |
Hi Sergei,
Thank you for the swift response:
The aBSREL tests were run in exploratory mode, so not sure if that will
have to be corrected within-gene for each branch, but BUSTED was
specifically testing whether one specific branch is inconsistent with model
that excludes positive selection (<40 gene of ~11k reject constrained
model). We also ran FUBAR because, if a gene got flagged as consistent with
positive selection in BUSTED, then I wanted to have the site-level tests
calculated already.
…On Tue, May 14, 2024 at 3:04 PM Sergei Pond ***@***.***> wrote:
Dear @NicMAlexandre <https://github.com/NicMAlexandre>,
There really isn’t anything formal that I ever wrote. Your specific
application matters quite a bit. Not knowing anything else, I would
recommend FDR for BUSTED. aBSREL is a bit more complicated, because it does
multiple testing correction at the level of branches for each run. You can
layer another correction on top of that if you want, probably another FDR.
Can you give me any details?
Best,
Sergei
—
Reply to this email directly, view it on GitHub
<#1707 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AFB633ZXWBRS2IBNSBQWYADZCJU47AVCNFSM6AAAAABHUN6WT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJRGA2DOOBQGE>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
--
Best,
Nicolas Alexandre
PhD Candidate, Integrative Biology
Whiteman Lab
University of California - Berkeley
***@***.*** ***@***.***>
|
Dear @NicMAlexandre,
Would you happen to have a list of p-values (for the 11k genes) that BUSTED produced that you could share? Best, |
Thank you, that makes complete sense. I just direct messaged the P-values. |
Hi Sergei,
Could you point me to a preferred method and rationale for multiple testing correction using BUSTED and absREL. I am having trouble finding these resources.
The text was updated successfully, but these errors were encountered: