Statistical test used in Custom Analysis (2-class comparison)

Q&A
1

I’ve used DepMap’s Custom Analysis 2-class comparison feature to compare three data types between two groups of cell lines :

  • CRISPR Chronos scores

  • Gene expression

  • Metabolite abundance

I have two specific questions for each of these analyses:

  1. What statistical test is used to compute the p-values, is it a simple two-sample t-test?

  2. What does the effect size represent , is it the difference in means between the two groups (e.g., difference in mean Chronos score, difference in mean log2 expression)?

I’m asking because I need to accurately describe the statistical methodology in a manuscript Methods section. Does the same statistical approach apply to all three data types, or does it differ depending on the data type being analyzed?