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Traditional multiple testing methods have limited ability to exploit such two-way grouping structure, leading to potential power loss.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a new 2D Group Benjamini\u2013Hochberg (2dGBH) procedure to harness the two-way grouping structure in omics data, extending the traditional one-way adaptive GBH procedure. Using both simulated and real datasets, we show that 2dGBH effectively controls the false discovery rate across biologically relevant settings, and it is more powerful than the BH or q-value procedure and more robust than the one-way adaptive GBH procedure.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>2dGBH is available as an R package at: https:\/\/github.com\/chloelulu\/tdGBH. The analysis code and data are available at: https:\/\/github.com\/chloelulu\/tdGBH-paper.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae035","type":"journal-article","created":{"date-parts":[[2024,1,21]],"date-time":"2024-01-21T01:14:28Z","timestamp":1705799668000},"source":"Crossref","is-referenced-by-count":13,"title":["2dGBH: Two-dimensional group Benjamini\u2013Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5234-3190","authenticated-orcid":false,"given":"Lu","family":"Yang","sequence":"first","affiliation":[{"name":"Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic , Rochester, MN 55905, United States"},{"name":"Center for Individualized Medicine, Mayo Clinic , Rochester, MN 55905, United 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