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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

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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
RNA-sequencing, Stage-wise testing, Differential transcript usage, Differential expression, RNA-SEQ ANALYSIS, PROSTATE-CANCER, MULTIPLE, HYPOTHESES, ASSOCIATION, TESTS, SETS

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Chicago
Van den Berge, Koen, Charlotte Soneson, Mark D Robinson, and Lieven Clement. 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.
APA
Van den Berge, K., Soneson, C., Robinson, M. D., & Clement, L. (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.
Vancouver
1.
Van den Berge K, Soneson C, Robinson MD, Clement L. stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. GENOME BIOLOGY. 2017;18.
MLA
Van den Berge, Koen et al. “stageR : a General Stage-wise Method for Controlling the Gene-level False Discovery Rate in Differential Expression and Differential Transcript Usage.” GENOME BIOLOGY 18 (2017): n. pag. Print.
@article{8528954,
  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.},
  articleno    = {151},
  author       = {Van den Berge, Koen and Soneson, Charlotte and Robinson, Mark D and Clement, Lieven},
  issn         = {1474-760X},
  journal      = {GENOME BIOLOGY},
  keywords     = {RNA-sequencing,Stage-wise testing,Differential transcript usage,Differential expression,RNA-SEQ ANALYSIS,PROSTATE-CANCER,MULTIPLE,HYPOTHESES,ASSOCIATION,TESTS,SETS},
  language     = {eng},
  pages        = {14},
  title        = {stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage},
  url          = {http://dx.doi.org/10.1186/s13059-017-1277-0},
  volume       = {18},
  year         = {2017},
}

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