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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology / methods*
  • Computer Simulation
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation
  • Genetic Association Studies / methods*
  • Humans
  • Reproducibility of Results
  • Sensitivity and Specificity