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Methods for large-scale statistical analyses have been developed but most of them are applicable to two-sample or two-condition data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed a large-scale multiple-group<jats:italic>F<\/jats:italic>-test based method, named ranking analysis of<jats:italic>F<\/jats:italic>-statistics (RAF), which is an extension of ranking analysis of microarray data (RAM) for two-sample t-test. In this method, we proposed a novel random splitting approach to generate the null distribution instead of using permutation, which may not be appropriate for microarray data. We also implemented a two-simulation strategy to estimate the false discovery rate. Simulation results suggested that it has higher efficiency in finding differentially expressed genes among multiple classes at a lower false discovery rate than some commonly used methods. By applying our method to the experimental data, we found 107 genes having significantly differential expressions among 4 treatments at &lt;0.7% FDR, of which 31 belong to the expressed sequence tags (ESTs), 76 are unique genes who have known functions in the brain or central nervous system and belong to six major functional groups.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our method is suitable to identify differentially expressed genes among multiple groups, in particular, when sample size is small.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-9-142","type":"journal-article","created":{"date-parts":[[2008,3,6]],"date-time":"2008-03-06T19:15:04Z","timestamp":1204830904000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Ranking analysis of F-statistics for microarray data"],"prefix":"10.1186","volume":"9","author":[{"given":"Yuan-De","family":"Tan","sequence":"first","affiliation":[]},{"given":"Myriam","family":"Fornage","sequence":"additional","affiliation":[]},{"given":"Hongyan","family":"Xu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,3,6]]},"reference":[{"issue":"4","key":"2127_CR1","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/ng1296-457","volume":"14","author":"J DeRisi","year":"1996","unstructured":"DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. 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