Methodology article

MAID : An effect size based model for microarray data integration across laboratories and platforms

Ivan Borozan¹ , Limin Chen^1,2 , Bryan Paeper⁷ , Jenny E Heathcote⁶ , Aled M Edwards^1,2,3 , Michael Katze⁷ , Zhaolei Zhang^1,2 and Ian D McGilvray^4,5

¹Banting and Best Department of Medical Research, University of Toronto, 112 College St, Toronto, ON M5G1L6, Canada

²Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S1A8, Canada

³Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G2M9, Canada

⁴Toronto General Research Institute, 610 University Avenue, Toronto, ON M5G2M9, Canada

⁵Department of Surgery, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S1A8, Canada

⁶Toronto Western Hospital, 399 Bathurst St, Toronto, ON M5T2S8, Canada

⁷Department of Microbiology, Box 357242, University of Washington, Seattle, WA 98195-7242, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:305doi:10.1186/1471-2105-9-305

Published:	10 July 2008

Abstract

Background

Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of microarray studies has increased, resulting in many different datasets available for any given disease. The increase in sensitivity and reliability of measurements of gene expression changes can be improved through a systematic integration of different microarray datasets that address the same or similar biological questions.

Results

Traditional effect size models can not be used to integrate array data that directly compare treatment to control samples expressed as log ratios of gene expressions. Here we extend the traditional effect size model to integrate as many array datasets as possible. The extended effect size model (MAID) can integrate any array datatype generated with either single or two channel arrays using either direct or indirect designs across different laboratories and platforms. The model uses two standardized indices, the standard effect size score for experiments with two groups of data, and a new standardized index that measures the difference in gene expression between treatment and control groups for one sample data with replicate arrays. The statistical significance of treatment effect across studies for each gene is determined by appropriate permutation methods depending on the type of data integrated. We apply our method to three different expression datasets from two different laboratories generated using three different array platforms and two different experimental designs. Our results indicate that the proposed integration model produces an increase in statistical power for identifying differentially expressed genes when integrating data across experiments and when compared to other integration models. We also show that genes found to be significant using our data integration method are of direct biological relevance to the three experiments integrated.

Conclusion

High-throughput genomics data provide a rich and complex source of information that could play a key role in deciphering intricate molecular networks behind disease. Here we propose an extension of the traditional effect size model to allow the integration of as many array experiments as possible with the aim of increasing the statistical power for identifying differentially expressed genes.