Header

UZH-Logo

Maintenance Infos

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage


Van den Berge, Koen; Soneson, Charlotte; Robinson, Mark D; Clement, Lieven (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology, 18(1):151.

Abstract

RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes. This method provides gene-level FDR control and boosts power for testing interaction effects. In transcript-level analysis, it provides a framework that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution. The procedure is applicable whenever individual hypotheses can be aggregated, providing a unified framework for complex high-throughput experiments.

Abstract

RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes. This method provides gene-level FDR control and boosts power for testing interaction effects. In transcript-level analysis, it provides a framework that performs powerful gene-level tests while maintaining biological interpretation at transcript-level resolution. The procedure is applicable whenever individual hypotheses can be aggregated, providing a unified framework for complex high-throughput experiments.

Statistics

Citations

Dimensions.ai Metrics
9 citations in Web of Science®
10 citations in Scopus®
3 citations in Microsoft Academic
Google Scholar™

Altmetrics

Downloads

49 downloads since deposited on 09 Jan 2018
32 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Molecular Life Sciences
Dewey Decimal Classification:570 Life sciences; biology
Scopus Subject Areas:Life Sciences > Ecology, Evolution, Behavior and Systematics
Life Sciences > Genetics
Life Sciences > Cell Biology
Language:English
Date:7 August 2017
Deposited On:09 Jan 2018 09:32
Last Modified:08 Apr 2020 22:24
Publisher:BioMed Central
ISSN:1474-7596
OA Status:Gold
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/s13059-017-1277-0
PubMed ID:28784146

Download

Gold Open Access

Download PDF  'stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage'.
Preview
Content: Published Version
Language: English
Filetype: PDF
Size: 2MB
View at publisher
Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)