Statistics or biology: the zero-inflation controversy about scRNA-seq data

被引：114

作者：

Jiang, Ruochen ^{[1
]}

Sun, Tianyi ^{[1
]}

Song, Dongyuan ^{[2
]}

Li, Jingyi Jessica ^{[1
,3
,4
,5
]}

机构：

[1] Univ Calif Los Angeles, Dept Stat, Los Angeles, CA 90095 USA

[2] Univ Calif Los Angeles, Bioinformat Interdept PhD Program, Los Angeles, CA 90095 USA

[3] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA 90095 USA

[4] Univ Calif Los Angeles, Dept Computat Med, Los Angeles, CA 90095 USA

[5] Univ Calif Los Angeles, Dept Stat, Los Angeles, CA 90095 USA

来源：

GENOME BIOLOGY | 2022年 / 23卷 / 01期

基金：

美国国家科学基金会;

关键词：

CELL GENE-EXPRESSION; SINGLE-CELL; RNA-SEQ; FATE DECISIONS; DNA; RECONSTRUCTION; AMPLIFICATION; IMPUTATION; BINDING; MODEL;

D O I：

10.1186/s13059-022-02601-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.

引用

页数：24

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