GilbertLabUCSF / ScreenPro2

[This is an archived repository, see the current version in Arc Institute GitHub]
https://github.com/ArcInstitute/ScreenPro2
MIT License
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Improve statistical test methods #19

Closed abearab closed 9 months ago

abearab commented 10 months ago

Current method:

https://screenpro2.readthedocs.io/en/latest/PhenoScore.html

Statistical test comparing y vs x per each target, T:

    \text{p-value}(T,x,y) = \text{t-test} \left(
    \begin{bmatrix}{N_{x}}\end{bmatrix}_{(a,b)},
    \begin{bmatrix}{N_{y}}\end{bmatrix}_{(a,b)}
    \right)

(see this wikipedia page: Dependent t-test for paired samples)

(see the link to the implemented tool: ttest_rel, a scipy module)


@mhorlbeck used Mann–Whitney U test in https://github.com/mhorlbeck/ScreenProcessing. The t-test approach here was originally extracted from @hanig's notebook in which he processed a V3 screen for his lab.

@AshirBorah has some ideas for assigning empirical p-values relative to negative control guides/oligos, we can discuss it here and implement it moving forward.