AbstractA key challenge in analyzing single cell RNA-sequencing data is the large number of false zeros, where genes actually expressed in a given cell are incorrectly measured as unexpressed. We present a method based on low-rank matrix approximation which imputes these values while preserving biologically non-expressed genes (true biological zeros) at zero expression levels. We provide theoretical justification for this denoising approach and demonstrate its advantages relative to other methods on simulated and biological datasets.
In this paper, we propose an error analysis of the generalized low-rank approximation, which is a generalization of the classical approximation of a matrix $A\in\mathbb{R}^{m\times n}$ by a matrix of a rank at most $r$, where $r\leq\min\{m,n\}$.
Zero-preserving imputation of single-cell RNA-seq data