Assessment of Single Cell RNA-Seq Normalization Methods

被引：7
|
作者：
Ding, Bo [1 ]
Zheng, Lina [1 ]
Wang, Wei [1 ,2 ]
机构：
[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Dept Cellular & Mol Med, La Jolla, CA 92093 USA
来源：
G3-GENES GENOMES GENETICS | 2017年 / 7卷 / 07期
基金：
美国国家卫生研究院;
关键词：
normalization; scRNA; statistical index; DIFFERENTIAL EXPRESSION ANALYSIS; HETEROGENEITY; NOISE;
D O I：
10.1534/g3.117.040683
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
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.
引用
收藏
页码：2039 / 2045
页数：7
相关论文
共 50 条
  • [1] Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
    Lytal, Nicholas
    Ran, Di
    An, Lingling
    FRONTIERS IN GENETICS, 2020, 11
  • [2] Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq
    Cole, Michael B.
    Risso, Davide
    Wagner, Allon
    DeTomaso, David
    Ngai, John
    Purdom, Elizabeth
    Dudoit, Sandrine
    Yosef, Nir
    CELL SYSTEMS, 2019, 8 (04) : 315 - +
  • [3] Normalization and noise reduction for single cell RNA-seq experiments
    Ding, Bo
    Zheng, Lina
    Zhu, Yun
    Li, Nan
    Jia, Haiyang
    Ai, Rizi
    Wildberg, Andre
    Wang, Wei
    BIOINFORMATICS, 2015, 31 (13) : 2225 - 2227
  • [4] Comparison of normalization methods for RNA-Seq data
    Aghababazadeh, Farnoosh A.
    Li, Qian
    Fridley, Brooke L.
    GENETIC EPIDEMIOLOGY, 2018, 42 (07) : 684 - 684
  • [5] SCnorm: robust normalization of single-cell RNA-seq data
    Bacher, Rhonda
    Chu, Li-Fang
    Leng, Ning
    Gasch, Audrey P.
    Thomson, James A.
    Stewart, Ron M.
    Newton, Michael
    Kendziorski, Christina
    NATURE METHODS, 2017, 14 (06) : 584 - +
  • [6] PsiNorm: a scalable normalization for single-cell RNA-seq data
    Borella, Matteo
    Martello, Graziano
    Risso, Davide
    Romualdi, Chiara
    BIOINFORMATICS, 2022, 38 (01) : 164 - 172
  • [7] SCnorm: robust normalization of single-cell RNA-seq data
    Rhonda Bacher
    Li-Fang Chu
    Ning Leng
    Audrey P Gasch
    James A Thomson
    Ron M Stewart
    Michael Newton
    Christina Kendziorski
    Nature Methods, 2017, 14 : 584 - 586
  • [8] The Impact of Normalization Methods on RNA-Seq Data Analysis
    Zyprych-Walczak, J.
    Szabelska, A.
    Handschuh, L.
    Gorczak, K.
    Klamecka, K.
    Figlerowicz, M.
    Siatkowski, I.
    BIOMED RESEARCH INTERNATIONAL, 2015, 2015
  • [9] Improved RNA-seq normalization
    Fletcher, Michael
    NATURE GENETICS, 2022, 54 (11) : 1584 - 1584
  • [10] Improved RNA-seq normalization
    Michael Fletcher
    Nature Genetics, 2022, 54 : 1584 - 1584
12345