Hi, I am trying to identify genes that are essential for my target cells. According to the introduction, if the score is close to -1, it means that the gene is essential for the cells. However, I have noticed that the score is often less than -1. How is this possible, and what does this mean? Additionally, if I want to identify the essential genes, what is the best threshold I should set to obtain meaningful results? Thanks.
If you’re interested in making a binary call on whether a gene is essential or not, you probably should use the “Probability of gene dependency” instead of “Gene Effect”.
See the the guidance at DepMap Genetic Dependencies FAQ for more explanation. (It was written when the method we used to compute “Gene Effect” was CERES and although we now use a newer method, Chronos, the advice given is still valid.)