so many zero p-values resulted from mageck mle

Question

[buffealo]

I am using mle function of mageck to generate CRISPR screen results bu when I look at p-values there are so many zeros.

This is a part of my gene summary file ,

what could be the problem? I appreciate any help. Thank you.

Answer 1

[ATpoint]

I've always found MLE to be quite a blackbox in terms of how it combines individual gRNAs into a single score. I would visualize the individual per-gRNA fold changes for a handful of genes and judge based on that whether these stats make sense. Maybe there's just a lot of evidence that these guides habe a strong effect here.

[buffealo]

Thank you so much for your answer