Stratified Test Alleviates Batch Effects in Single-Cell Data

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 si...

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Detalles Bibliográficos
Autores principales: Liang, Shaoheng, Liang, Qingnan, Chen, Rui, Chen, Ken
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197071/
http://dx.doi.org/10.1007/978-3-030-42266-0_13
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author Liang, Shaoheng
Liang, Qingnan
Chen, Rui
Chen, Ken
author_facet Liang, Shaoheng
Liang, Qingnan
Chen, Rui
Chen, Ken
author_sort Liang, Shaoheng
collection PubMed
description 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.
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spelling pubmed-71970712020-05-04 Stratified Test Alleviates Batch Effects in Single-Cell Data Liang, Shaoheng Liang, Qingnan Chen, Rui Chen, Ken Algorithms for Computational Biology Article 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. 2020-02-01 /pmc/articles/PMC7197071/ http://dx.doi.org/10.1007/978-3-030-42266-0_13 Text en © Springer Nature Switzerland AG 2020 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
Liang, Shaoheng
Liang, Qingnan
Chen, Rui
Chen, Ken
Stratified Test Alleviates Batch Effects in Single-Cell Data
title Stratified Test Alleviates Batch Effects in Single-Cell Data
title_full Stratified Test Alleviates Batch Effects in Single-Cell Data
title_fullStr Stratified Test Alleviates Batch Effects in Single-Cell Data
title_full_unstemmed Stratified Test Alleviates Batch Effects in Single-Cell Data
title_short Stratified Test Alleviates Batch Effects in Single-Cell Data
title_sort stratified test alleviates batch effects in single-cell data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197071/
http://dx.doi.org/10.1007/978-3-030-42266-0_13
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AT chenken stratifiedtestalleviatesbatcheffectsinsinglecelldata

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