Crispr (Avana) Public 20Q3 scores


I have a question about scores that are given in Crispr (Avana) Public 20Q3. The gene of my interest gives scores from -1.3 to 0.36 in different cell lines after Crispr knockout. What these scores technically mean? Should I consider all cell lines below 0 as affected (=showing growth problems)? And those giving scores above 0 as feeling better after knockout (growing faster=not negativelly affected)?

And when I look for biomarkers which classify lines into sensitive or insensitive should I use -0.5 as a border or AM or 0 could also make sence to be used to count p-value?

Thank you in advance,


Hi Darya,

It does not sound like you have much of an outgrowth at only +0.36. If you want a binary label of cells being negatively affected, I would use Gene Dependency scores, which are the probability that a given gene effect represents a true depleting effects. For a classifier, you can choose whatever probability threshold you want in gene dependency based on the balance you want between false positives and false negatives.

I’m an undergrad student, hoping you can help me. When I downloaded the dataset, CRISPR (Avana) Public 20Q4 how can I use R to compare the Gene Effect scores (CERES) of a certain mutation to all other cell lines because I downloaded the data and the spreadsheets first column is the name of cell lines in which are not the numeric scores. How can I compare the CERES scores using R?

Hi Carolina,

This sounds like a pretty general question about how to use R, which is beyond the scope of things we can help with.