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

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.

SUBMITTER: Van den Berge K

PROVIDER: S-EPMC5547545 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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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 K Soneson Charlotte C Robinson Mark D MD Clement Lieven L

Genome biology 20170807 1

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 analys ...[more]

PMID: 28784146

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