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Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB

BMC bioinformatics 2009年第1期10卷 354-354页

作者： Chatziioannou, Aristotelis Moulos, Panagiotis Kolisis, Fragiskos N. Natl Hellen Res Fdn Inst Biol Res & Biotechnol Metab Engn & Bioinformat Grp Athens 11635 Greece

Background: The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. Results: We describe here Gene ARMADA ( Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form ( Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and bioinformatics toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime. Concl

关键词： Microarray Dataset Microarray Data Analysis Affymetrix Array Data Analysis Structure bioinformatics toolbox

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关键词： MATLAB bioinformatics toolbox

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