Extended Data Fig. 2: Additional analytical results from the CS Cell Painting benchmark.
From: Scalable, compressed phenotypic screening using pooled perturbations
a. Bar graph of top and bottom 10 perturbations in GT screen by mean cell number across n = 6 replicate wells with that perturbation. Error bar indicates 95% confidence interval. b. Histogram of cell number distribution in perturbation wells, stratified by extent of compression. Coefficient of variance (CV; std./mean) = 0.088, R2 = 0.037 amongst compressed run mean cell counts; CV = 0.22, R2 = 0.048 amongst uncompressed and compressed run mean cell count. c. Histogram of cell number distribution in GT perturbation wells stratified by whether the perturbation was identified as a hit in the compressed screen. d. Comparison of different statistical methods to evaluate the correlation of effect sizes between GT and CS. Error bar indicates 95% confidence interval. e. Scatterplot of correlation between effect sizes (L1 norms of regression coefficients) in two CS runs (permutation test, p-value < 0.01. f. Using GT screen significant perturbations as ground truth, ROC curves (true positive rate vs. false positive rate) show the performance of the CS screens in run 2 for correctly identifying hits at each pool size while varying the permutation testing threshold (from 0 to 1 in steps of 0.01) in the deconvolution algorithm.
