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Contributions of the EMERALD project to assessing and improving microarray data quality

Published

Author(s)

Vidar Beisvag, Audrey Kauffmann, James Malone, Carole Foy, Marc L. Salit, Schimmel Heinz, Erik Bongcam-Rudloff, Ulf Landegren, Helen Parkinson, Wolfgang Huber, Alvis Brazma, Arne K. Sandvik, Martin Kuiper

Abstract

While MIAME standards have helped to increase the value of microarray data deposited in public databases like ArrayExpress and GEO, limited means have been available to assess the quality of the data or to identify the procedures that were used to normalise and transform raw data. The EMERALD FP6 Coordination Action was designed to deliver means to assess and enhance the overall quality of microarray data, and to disseminate these means to the microarray community through an extensive series of workshops, tutorials and symposia. Tools were developed for assessing data quality, and used to demonstrate how removing data of poor quality could improve the power of statistical analyses and facilitate the analysis of multiple joint microarray datasets. These quality metrics tools are disseminated through publications and in particular through the software package arrayQualityMetrics. Within the framework provided by the Ontology of Biomedical Investigations ontologies were developed to describe data transformations and a software ontology to describe gene expression analysis software. In addition, the consortium advocated the development and use of external reference standards in microarray hybridisations, and created the Molecular Methods database MolMeth, which provides a central source of methods and protocols with a special focus on microarray-based technologies.
Citation
Biotechniques
Volume
50
Issue
1

Keywords

microarray data, quality metrics, ontology, protocols, standards, external standards, meta-analysis

Citation

Beisvag, V. , Kauffmann, A. , Malone, J. , Foy, C. , Salit, M. , Heinz, S. , Bongcam-Rudloff, E. , Landegren, U. , Parkinson, H. , Huber, W. , Brazma, A. , Sandvik, A. and Kuiper, M. (2011), Contributions of the EMERALD project to assessing and improving microarray data quality, Biotechniques, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=907567 (Accessed April 15, 2024)
Created December 31, 2010, Updated October 12, 2021