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Improve statistical test methods #19

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abearab opened this issue Nov 3, 2023 · 0 comments
Closed

Improve statistical test methods #19

abearab opened this issue Nov 3, 2023 · 0 comments
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enhancement New feature or request help wanted Extra attention is needed

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@abearab
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abearab commented Nov 3, 2023

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.

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