Fig. 3: The mAP framework applied to morphological profiling of CRISPR-Cas9 knockout perturbations (Cell Health dataset).

A mAP is calculated to assess well position and individual plate effects on phenotypic activity by retrieving guide replicates against controls in three scenarios (replicates of a guide across different plates and well positions; replicates of a guide across different plates, but in the same well position; and replicates of a guide within the same plate, but in different well position) and two data preprocessing methods (standardize and MAD robustize per plate). Percentages retrieved indicate the percentage of scores with p-value below 0.05 per cell line (and averaged across all cell lines in parenthesis). B mAP is calculated to assess the phenotypic activity of perturbations by guide replicate retrievability against controls in three cell lines individually (49% retrieved on average across all three cell lines). Results included all three replicate plates available per cell line. C Replicate-level AP scores calculated for a subset of guides from (B) highlight the variation from guide to guide across cell lines. D mAP p-values estimated to assess the influence of individual fluorescence channels on guide phenotypic activity against controls by either dropping a channel or including only that single channel (percent retrieved is shown for each axis); these results can be compared to 49% retrieved when all channels’ data is available (on average across all three cell lines, as in B). E mAP is calculated to assess the phenotypic consistency of guides annotated with related target genes (against guides annotated with other genes) in three cell lines individually. F Guide-level AP scores calculated for a subset of genes from (E) highlight the variation from gene to gene  across cell lines. mAP p-values were estimated using a one-sided permutation test and adjusted for multiple comparisons by Benjamini–Hochberg procedure. Percent retrieved indicates the percentage of scores with p-value below 0.05. Source data are provided as a Source Data file.