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Fig. 2 | Genome Biology

Fig. 2

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

Fig. 2

We fit NB regression models for each gene individually and bootstrapped the process to measure uncertainty in the resulting parameter estimates. a Model parameters for 16,809 genes for the NB regression model, plotted as a function of average gene abundance across the 33,148 cells. The color of each point indicates a parameter uncertainty score as determined by bootstrapping (“Methods” section). Pink line shows the regularized parameters obtained via kernel regression. b Standard deviation (σ) of NB regression model parameters across multiple bootstraps. Red points: σ for unconstrained NB model. Blue points: σ for regularized NB model, which is substantially reduced in comparison. Black trendline shows an increase in σ for low-abundance genes, highlighting the potential for overfitting in the absence of regularization

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