p-values or FDR

[jeslipp]

Thank you for providing this tool. I would be interested to know if the p-values reported in the output files are raw p-values or corrected p-values. I was unable to find a documentation of the output file and it was not clear to me from the methods in the paper.

Thanks for your time!

[lp2]

To the best of my knowledge, the p-values are uncorrected, but the FDR cutoffs are ; Felicity will know better. The relevant code is here: https://github.com/felicityallen/JACKS/blob/master/jacks/jacks/jacks_io.py#L68 and the relevant lines are 83 and 84 [JACKS posterior of w is evaluated against non-essential genes, and FDRs calculated]. Leo

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On Mon, Mar 23, 2020 at 9:26 AM Jesse Lipp ***@***.***> wrote: Thank you for providing this tool. I would be interested to know if the p-values reported in the output files are raw p-values or corrected p-values. I was unable to find a documentation of the output file and it was not clear to me from the methods in the paper. Thanks for your time! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADIQI6OALOVB5WT4DCYMR3RI4TLJANCNFSM4LRXAPAA> .

[felicityallen]

Sorry for my slow response, what Leo said is correct.

[jeslipp]

Thank you for the clarification!