Format

Send to

Choose Destination
Genome Biol. 2017 Aug 7;18(1):151. doi: 10.1186/s13059-017-1277-0.

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

Author information

1
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, S9, Ghent, 9000, Belgium.
2
Bioinformatics Institute Ghent, Ghent University, Ghent, 9000, Belgium.
3
Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
4
SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland.
5
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, S9, Ghent, 9000, Belgium. lieven.clement@ugent.be.
6
Bioinformatics Institute Ghent, Ghent University, Ghent, 9000, Belgium. lieven.clement@ugent.be.

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.

KEYWORDS:

Differential expression; Differential transcript usage; RNA-sequencing; Stage-wise testing

PMID:
28784146
PMCID:
PMC5547545
DOI:
10.1186/s13059-017-1277-0
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center