Journal
GENOME BIOLOGY
Volume 18, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-017-1277-0
Keywords
RNA-sequencing; Stage-wise testing; Differential transcript usage; Differential expression
Funding
- Belgian government (Belgian Science Policy) [P7/06]
- Ghent University
- Research Foundation - Flanders (FWO)
- Forschungskredit of the University of Zurich [FK-16-107]
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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.
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