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Open Access Highly Accessed Methodology article

Robust test method for time-course microarray experiments

Insuk Sohn13*, Kouros Owzar23, Stephen L George23, Sujong Kim4 and Sin-Ho Jung23

Author Affiliations

1 Biostatistics and Bioinformatics Center, Samsung Cancer Research Institute, Samsung Medical Center, Seoul, 137-710, Republic of Korea

2 Department of Biostatistics and Bioinformatics, Duke University Medical Center, NC 27710, USA

3 CALGB Statistical Center, NC 27710, USA

4 R&D Center, Komipharm International Co., LTD, Kyounggi-do 429-450, Republic of Korea

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BMC Bioinformatics 2010, 11:391  doi:10.1186/1471-2105-11-391

Published: 22 July 2010

Abstract

Background

In a time-course microarray experiment, the expression level for each gene is observed across a number of time-points in order to characterize the temporal trajectories of the gene-expression profiles. For many of these experiments, the scientific aim is the identification of genes for which the trajectories depend on an experimental or phenotypic factor. There is an extensive recent body of literature on statistical methodology for addressing this analytical problem. Most of the existing methods are based on estimating the time-course trajectories using parametric or non-parametric mean regression methods. The sensitivity of these regression methods to outliers, an issue that is well documented in the statistical literature, should be of concern when analyzing microarray data.

Results

In this paper, we propose a robust testing method for identifying genes whose expression time profiles depend on a factor. Furthermore, we propose a multiple testing procedure to adjust for multiplicity.

Conclusions

Through an extensive simulation study, we will illustrate the performance of our method. Finally, we will report the results from applying our method to a case study and discussing potential extensions.