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An interactive, easy to use application seems therefore necessary to help researchers to extract full information from data and analyse them in a simple, powerful and confident way.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>PreP+07 is a standalone Windows XP application that presents a friendly interface for spot filtration, inter- and intra-slide normalization, duplicate resolution, dye-swapping, error removal and statistical analyses. Additionally, it contains two unique implementation of the procedures \u2013 double scan and Supervised Lowess-, a complete set of graphical representations \u2013 MA plot, RG plot, QQ plot, PP plot, PN plot \u2013 and can deal with many data formats, such as tabulated text, GenePix GPR and ArrayPRO. PreP+07 performance has been compared with the equivalent functions in Bioconductor using a tomato chip with 13056 spots. The number of differentially expressed genes considering p-values coming from the PreP+07 and Bioconductor Limma packages were statistically identical when the data set was only normalized; however, a slight variability was appreciated when the data was both normalized and scaled.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>PreP+07 implementation provides a high degree of freedom in selecting and organizing a small set of widely used data processing protocols, and can handle many data formats. Its reliability has been proven so that a laboratory researcher can afford a statistical pre-processing of his\/her microarray results and obtain a list of differentially expressed genes using PreP+07 without any programming skills. All of this gives support to scientists that have been using previous PreP releases since its first version in 2003.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-10-16","type":"journal-article","created":{"date-parts":[[2009,1,13]],"date-time":"2009-01-13T07:12:58Z","timestamp":1231830778000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data"],"prefix":"10.1186","volume":"10","author":[{"given":"Victoria","family":"Martin-Requena","sequence":"first","affiliation":[]},{"given":"Antonio","family":"Mu\u00f1oz-Merida","sequence":"additional","affiliation":[]},{"given":"M Gonzalo","family":"Claros","sequence":"additional","affiliation":[]},{"given":"Oswaldo","family":"Trelles","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,1,12]]},"reference":[{"key":"2746_CR1","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/S1016-8478(23)17418-8","volume":"22","author":"JinHwan Do","year":"2006","unstructured":"Do Jin, Choi Dong-Kug: Normalization of microarray data: single-labeled and dual-labeled arrays. 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