Benjamini-Hochberg FDR calculation

ArcInstitute / ScreenPro2

Flexible analysis of high-content CRISPR screening

https://screenpro2.rtfd.io

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Benjamini-Hochberg FDR calculation #11

Closed abearab closed 8 months ago

abearab commented 11 months ago

[x] Simple Benjamini-Hochberg FDR calculation from p-values

root – https://github.com/GilbertLabUCSF/ScreenPro2/issues/21

abearab commented 11 months ago

Charlene Pan from UCSF

the output BH column was all NAs because some genes had 0 inputs, so I changed the change L40 of screenpro.init.py to fill in the nan p-values: p_values[pd.isna(p_values)] = 1 to get it working; but alternatively I think changing my count matrix df[df == 0] = 1 works too

solved here 44ca6954fbd42af50f1bc5ed7c02a85bdb98f6f1