Stratified Test Alleviates Batch Effects in Single-Cell Data

Shaoheng Liang; Qingnan Liang; Rui Chen; Ken Chen

doi:10.1007/978-3-030-42266-0_13

Stratified Test Alleviates Batch Effects in Single-Cell Data

Shaoheng Liang, Qingnan Liang, Rui Chen, Ken Chen

Bioinformatics & Computational Biology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

Analyzing single-cell sequencing data across batches is challenging. We find that the Van Elteren test, a stratified version of Wilcoxon rank-sum test, elegantly mitigates the problem. We also modified the common language effect size to supplement this test, further improving its utility. On both simulated and real patient data we show the ability of Van Elteren test to control for false positives and false negatives. The effect size also estimates the differences between cell types more accurately.

Original language	English (US)
Title of host publication	Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings
Editors	Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler
Publisher	Springer
Pages	167-177
Number of pages	11
ISBN (Print)	9783030422653
DOIs	https://doi.org/10.1007/978-3-030-42266-0_13
State	Published - 2020
Event	7th International Conference on Algorithms for Computational Biology, AlCoB 2020 - Missoula, United States Duration: Apr 13 2020 → Apr 15 2020

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	12099 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	7th International Conference on Algorithms for Computational Biology, AlCoB 2020
Country/Territory	United States
City	Missoula
Period	4/13/20 → 4/15/20

Keywords

Batch effect
Differential expression analysis
Van Elteren test
Wilcoxon rank-sum test
scRNA-seq analysis

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-030-42266-0_13

Cite this

Liang, S., Liang, Q., Chen, R., & Chen, K. (2020). Stratified Test Alleviates Batch Effects in Single-Cell Data. In C. Martín-Vide, M. A. Vega-Rodríguez, & T. Wheeler (Eds.), Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings (pp. 167-177). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12099 LNBI). Springer. https://doi.org/10.1007/978-3-030-42266-0_13

Stratified Test Alleviates Batch Effects in Single-Cell Data. / Liang, Shaoheng; Liang, Qingnan; Chen, Rui et al.
Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings. ed. / Carlos Martín-Vide; Miguel A. Vega-Rodríguez; Travis Wheeler. Springer, 2020. p. 167-177 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12099 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Liang, S, Liang, Q, Chen, R & Chen, K 2020, Stratified Test Alleviates Batch Effects in Single-Cell Data. in C Martín-Vide, MA Vega-Rodríguez & T Wheeler (eds), Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12099 LNBI, Springer, pp. 167-177, 7th International Conference on Algorithms for Computational Biology, AlCoB 2020, Missoula, United States, 4/13/20. https://doi.org/10.1007/978-3-030-42266-0_13

Liang S, Liang Q, Chen R, Chen K. Stratified Test Alleviates Batch Effects in Single-Cell Data. In Martín-Vide C, Vega-Rodríguez MA, Wheeler T, editors, Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings. Springer. 2020. p. 167-177. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-42266-0_13

Liang, Shaoheng ; Liang, Qingnan ; Chen, Rui et al. / Stratified Test Alleviates Batch Effects in Single-Cell Data. Algorithms for Computational Biology - 7th International Conference, AlCoB 2020, Proceedings. editor / Carlos Martín-Vide ; Miguel A. Vega-Rodríguez ; Travis Wheeler. Springer, 2020. pp. 167-177 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Stratified Test Alleviates Batch Effects in Single-Cell Data

Abstract

Publication series

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Keywords

ASJC Scopus subject areas

Access to Document

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