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The aim of this paper is to discuss the impact of normalisation techniques for two-channel array technology on the process of identification of differentially expressed genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Through three precise simulation plans, we quantify the impact of normalisations: (a) on the sensitivity and specificity of a specified test statistic for the identification of deregulated genes, (b) on the gene ranking induced by the statistic.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Although we found a limited difference of sensitivities and specificities for the test after each normalisation, the study highlights a strong impact in terms of gene ranking agreement, resulting in different levels of agreement between competing normalisations. However, we show that the combination of two normalisations, such as glog and lowess, that handle different aspects of microarray data, is able to outperform other individual techniques.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-10-61","type":"journal-article","created":{"date-parts":[[2009,2,13]],"date-time":"2009-02-13T19:13:28Z","timestamp":1234552408000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["A comparison on effects of normalisations in the detection of differentially expressed genes"],"prefix":"10.1186","volume":"10","author":[{"given":"Monica","family":"Chiogna","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Sofia","family":"Massa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Davide","family":"Risso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,2,13]]},"reference":[{"issue":"6","key":"2791_CR1","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1038\/35076576","volume":"2","author":"J Quackenbush","year":"2001","unstructured":"Quackenbush J: Computational analysis of microarray data. 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