Fig. 3.

Analysis results for the mESCs data: (A) t-SNE plots of the sample patterns from uncorrected data (normalized raw count data), ComBat-corrected data, MNN-corrected data, scBatch-corrected data, limma-corrected data, rescaleBatches-corrected data and scPLS-corrected data, colored by different cultured conditions; (B) comparison of the significant genes from pairwise differential-gene tests by Seurat (Satija et al., 2015) with adjusted P-values $<{10}^{-6}$ and log fold-changes >2