Mathbio Seminar

Speaker: Akshay Parokari
Title: Feature Selection and Dimension Reduction for Single-Cell RNA-Seq Based on a Multinomal Model
Abstract: Single-cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow multinomial sampling with no zero inflation. Current normalization procedures such as a log of counts per million and feature selection by highly variable genes produce false variability in dimension reduction. We propose simple multinomial methods, including generalized principal component analysis (GLM-PCA) for non-normal distributions, and feature selection using deviance. These methods outperform the current practice in a downstream clustering assessment using ground truth datasets.