Supplementary Figure 3: Simulation of equally sized batches with one having additional noise.
From: A test metric for assessing single-cell RNA-seq batch correction
Additional noise is a factor multiplied on final gene expression means and is drawn from a log normal distribution LN, with batch factor and batch scale .We simulated 1,000 samples and drew subsets from this dataset. Batches were always equally sized. (a-b) Batch-effect analysis for several batch factors (a) and batch scales (b) using kBET, PC regression (variance explained by batch effect) and silhouette coefficients (from top to bottom). kBET rejection rates were computed for both the original data space and the default 50-dimensional PC space (top two plots). (c-d) Mean relation (top), dropout relation (center), PCA plot for batch factor = 0.1 (c) and a batch scale = 0.5 (d). Blue lines indicate the linear fit with parameters depicted in the top left corner. R2 values denote the variance explained by the fit and correspond to high correlation of mean and dropout of both batches.
