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Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-seq

By Michael B Cole, Davide Risso, Allon Wagner, David DeTomaso, John Ngai, Elizabeth Purdom, Sandrine Dudoit, Nir Yosef

Posted 16 Dec 2017
bioRxiv DOI: 10.1101/235382 (published DOI: 10.1016/j.cels.2019.03.010)

Systematic measurement biases make data normalization an essential preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple, competing considerations behind the assessment of normalization performance, some of them study-specific. Because normalization can have a large impact on downstream results (e.g., clustering and differential expression), it is critically important that practitioners assess the performance of competing methods. We have developed scone - a flexible framework for assessing normalization performance based on a comprehensive panel of data-driven metrics. Through graphical summaries and quantitative reports, scone summarizes performance trade-offs and ranks large numbers of normalization methods by aggregate panel performance. The method is implemented in the open-source Bioconductor R software package scone. We demonstrate the effectiveness of scone on a collection of scRNA-seq datasets, generated with different protocols, including Fluidigm C1 and 10x platforms. We show that top-performing normalization methods lead to better agreement with independent validation data.

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