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Open Access Highly Accessed Research article

Comparison study of microarray meta-analysis methods

Anna Campain* and Yee Hwa Yang

Author Affiliations

School of Mathematics and Statistics, Center of Mathematical Biology, University of Sydney, F07 Sydney, NSW 2006, Australia

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BMC Bioinformatics 2010, 11:408  doi:10.1186/1471-2105-11-408

Published: 3 August 2010



Meta-analysis methods exist for combining multiple microarray datasets. However, there are a wide range of issues associated with microarray meta-analysis and a limited ability to compare the performance of different meta-analysis methods.


We compare eight meta-analysis methods, five existing methods, two naive methods and a novel approach (mDEDS). Comparisons are performed using simulated data and two biological case studies with varying degrees of meta-analysis complexity. The performance of meta-analysis methods is assessed via ROC curves and prediction accuracy where applicable.


Existing meta-analysis methods vary in their ability to perform successful meta-analysis. This success is very dependent on the complexity of the data and type of analysis. Our proposed method, mDEDS, performs competitively as a meta-analysis tool even as complexity increases. Because of the varying abilities of compared meta-analysis methods, care should be taken when considering the meta-analysis method used for particular research.