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We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information\/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Performance analysis refined the results from benchmarks published previously.<\/jats:p>\n            <jats:p>We show that the Shrinkage <jats:italic>t<\/jats:italic> test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized <jats:italic>t<\/jats:italic> test and the Window <jats:italic>t<\/jats:italic> test performed slightly better.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>The R scripts used for the analysis are available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/urbm-cluster.urbm.fundp.ac.be\/~bdemeulder\/\" ext-link-type=\"uri\">http:\/\/urbm-cluster.urbm.fundp.ac.be\/~bdemeulder\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-17","type":"journal-article","created":{"date-parts":[[2010,1,12]],"date-time":"2010-01-12T07:14:52Z","timestamp":1263280492000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["A benchmark for statistical microarray data analysis that preserves actual biological and technical variance"],"prefix":"10.1186","volume":"11","author":[{"given":"Beno\u00eet","family":"De Hertogh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertrand","family":"De Meulder","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabrice","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Pierre","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Bareke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthoula","family":"Gaigneaux","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Depiereux","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,1,11]]},"reference":[{"issue":"1","key":"3474_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/biomet\/6.1.1","volume":"6","author":"Student","year":"1908","unstructured":"Student: The Probable Error of Mean. 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