ArticleBMC bioinformatics2009
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit.BMC genomics · 2012Article
- Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis.Journal of bacteriology · 2011Article
- Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis.Plant physiology · 2010Article
- Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.BMC bioinformatics · 2009Article
- Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA-AFLP).Electrophoresis · 2009Article
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4 authors.
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Abstract
backgroundNowadays, microarray gene expression analysis is a widely used technology that scientists handle but whose final interpretation usually requires the participation of a specialist. The need for this participation is due to the requirement of some background in statistics that most users lack or have a very vague notion of. Moreover, programming skills could also be essential to analyse these data. 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.
resultsPreP+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 - double scan and Supervised Lowess-, a complete set of graphical representations - MA plot, RG plot, QQ plot, PP plot, PN plot - 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.
conclusionPreP+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.
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