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Integrating data from heterogeneous DNA microarray platforms

Valente, Eduardo ; Rocha, Miguel

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Valente, Eduardo ; Rocha, Miguel  (2015)  Integrating data from heterogeneous DNA microarray platforms. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 12(4): Special Issue: Selected extended papers of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, Spain, 2015. Guest editors: Florentino Fdez-Riverola, Juan F. De Paz, Ross Overbeek and Miguel Rocha

Online-Journal: http://journal.imbio.de/
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2015/5420



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