Fig. 1
From: Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Performance of existing normalization methods on the simulated data with DE genes and stochastic zeroes. The size factor estimates for all cells are plotted against the true values for a DESeq, b TMM, and c library size normalization. Simulations were performed with no DE (first row), moderate DE (second row), strong DE (third row), and varying magnitudes of DE (fourth row). Axes are shown on a log-scale. For comparison, each set of size factors was scaled such that the grand mean across cells was the same as that for the true values. The red line represents equality between the rescaled estimates and true factors. Cells in the first, second, and third subpopulations are shown in black, blue, and orange, respectively. DE differentially expressed, TMM trimmed mean of M values