ArticleBioinformatics (Oxford, England)2021
The optimal discovery procedure for significance analysis of general gene expression studies.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Perspectives on rigor and reproducibility in single cell genomics.PLoS genetics · 2022Article
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2 authors.
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Abstract
motivationAnalysis of biological data often involves the simultaneous testing of thousands of genes. This requires two key steps: the ranking of genes and the selection of important genes based on a significance threshold. One such testing procedure, called the optimal discovery procedure (ODP), leverages information across different tests to provide an optimal ranking of genes. This approach can lead to substantial improvements in statistical power compared to other methods. However, current applications of the ODP have only been established for simple study designs using microarray technology. Here, we extend this work to the analysis of complex study designs and RNA-sequencing studies.
resultsWe apply our extended framework to a static RNA-sequencing study, a longitudinal study, an independent sampling time-series study,and an independent sampling dose-response study. Our method shows improved performance compared to other testing procedures, finding more differentially expressed genes and increasing power for enrichment analysis. Thus, the extended ODP enables a favorable significance analysis of genome-wide gene expression studies. AVAILABILITY AND IMPLEMENTATION: The algorithm is implemented in our freely available R package called edge and can be downloaded at https://www.bioconductor.org/packages/release/bioc/html/edge.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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