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Fig. 6 | Genome Biology

Fig. 6

From: Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Fig. 6

Downstream analyses of Pearson residuals are unaffected by differences in sequencing depth. a UMAP embedding of the 33,148 cell PBMC dataset using either log-normalization or Pearson residuals. Both normalization schemes lead to similar results with respect to the major and minor cell populations in the dataset. However, in analyses of log-normalized data, cells within a cluster are ordered along a gradient that is correlated with sequencing depth. b Within the four major cell types, the percent of variance explained by sequencing depth under both normalization schemes. c UMAP embedding of two groups of biologically identical CD14+ monocytes, where one group was randomly downsampled to 50% depth. d Results of differential expression (DE) test between the two groups shown in c. Gray areas indicate expected group mean difference by chance and a false discovery rate cutoff of 1%. e Results of DE test between CD14+ and CD16+ monocytes, before and after randomly downsampling the CD16+ cells to 20% depth

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