Extended Data Fig. 9: Comparison of output summarization methods for constructing an integer count matrix. | Nature Methods

Extended Data Fig. 9: Comparison of output summarization methods for constructing an integer count matrix.

From: Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

Extended Data Fig. 9

Methods are discussed in Supplementary Sections 5.5 (legend label MCKP), 5.6 (legend label Posteior CDF), and 5.7 (legend labels PR-μ and PR-q). The four panels show four different ways to compute TPR and FPR to display a ROC curve. “Macro-averaged per cell” computes TPR as (∑gTPng)/(∑gTPng + FNng), while “micro-averaged per cell" computes TPR as ∑g[TPng/(TPng + FNng)]. For the “per gene” cases, the sum over genes is replaced by a sum over cells. We exclude genes whose raw data counts are less than 10 summed over all cells. The dots shown represent the mean over all cells or genes as appropriate.

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