Extended Data Fig. 2: Outlier pool QC filter to detect pool-level failures.

a, Primary screen QC pass rate by pool. The fraction of treated assay plate-wells that pass the outlier filter is indicated. Cell line log MFI data are median-centered, and the medians of assay plate-wells are compared within each well-detection plate combination. Extreme outliers with |robust z-score| >5 are filtered. b, Primary screen QC pass rate by detection plate. c, Primary screen QC pass rate of assay plates. Overall pass rate was high (median 98.6%, minimum 83.8%). d, Secondary screen QC pass rate by pool. e, Secondary screen QC pass rate by detection plate. The pass rate is above 95% for 81% of detection plates. f, Secondary screen QC pass rate by plate-pool combinations. 3 replicate plates are combined for visualization. Overall pass rate was high (median 99.1%, mean 94.3%), where failures are almost exclusively coming from 7 detection plates, implying failure at final detection step. Across the screen, 5.7% of the pools are filtered out as outliers.