Assessment of Single Cell RNA-Seq Normalization Methods

Bo Ding; Lina Zheng; Wei Wang

doi:10.1534/g3.117.040683

Assessment of Single Cell RNA-Seq Normalization Methods

G3 (Bethesda). 2017 Jul 5;7(7):2039-2045. doi: 10.1534/g3.117.040683.

Authors

Bo Ding¹, Lina Zheng¹, Wei Wang^{1

2}

Affiliations

¹ Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359 wei-wang@ucsd.edu.
² Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093-0359.

Abstract

We have assessed the performance of seven normalization methods for single cell RNA-seq using data generated from dilution of RNA samples. Our analyses showed that methods considering spike-in External RNA Control Consortium (ERCC) RNA molecules significantly outperformed those not considering ERCCs. This work provides a guidance of selecting normalization methods to remove technical noise in single cell RNA-seq data.

Keywords: normalization; scRNA; statistical index.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

High-Throughput Nucleotide Sequencing / methods*
High-Throughput Nucleotide Sequencing / standards
Models, Genetic*
Sequence Analysis, RNA / methods*
Sequence Analysis, RNA / standards

Abstract

Publication types

MeSH terms

Grants and funding