A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments
Fig 5
Assessment of hit calling pipelines.
The figure (A) shows a single batch of simulated arrayed CRISPR screening data with 4 plates. Plate 3 and 4 were chosen to be affected by plate effects and spatial bias. The plate effect was generated by increasing the overall signals with pre-defined amount. The spatial bias was generated with the same approach as in Fig 4. Each dot represents the endpoint value of each well, and blue dots correspond to the one with spatial bias. The figures (B-D) show the distribution of True Positive Rates (TPR), Positive Predictive Value (PPV) and F1 score for 6 workflows. Each dot corresponds to TPR, PPV or F1 value for a simulated screen dataset of 4 plates, and the simulation was repeated 100 times.