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A Two-Stage Procedure for the Removal of Batch Effects in Microarray Studies

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Abstract

The presence of different batches is routinely observed in microarray studies and is well known that non-biological variability potentially confounding biological differences is commonly related to such batches. The removal of these undesired effects for a non-biased inference is often accomplished either with normalization methods that do not take into account all the available information, or with models that rely on strong parametric assumptions. We have developed a new method for the batch effects removal, named ber, which is based on a two-stage procedure for the estimation of location and scale parameters. Batch effects and biological differences are estimated using a regression approach and bagging, therefore mild distributional assumptions are required. We have compared ber with other commonly employed methods and we have shown that ber can bring to a higher power in detecting differentially expressed genes. The application of ber to a real microarray study led to interpretable biological results. The method is implemented in the R package ber, available through CRAN repository.

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Acknowledgements

The author is grateful to two referees for the helpful comments and valuable suggestions. The author wants to thank Mahmoodi Pezhman, Andrea Zangrando and Pietro Franceschi for the careful reading of the manuscript. This work was supported by Fondazione Cittá della Speranza.

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  1. Department for Woman and Child’s Health, University of Padua, Via Giustiniani 3, Padova, Italy

    Marco Giordan

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  1. Marco Giordan
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Correspondence to Marco Giordan.

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Giordan, M. A Two-Stage Procedure for the Removal of Batch Effects in Microarray Studies. Stat Biosci 6, 73–84 (2014). https://doi.org/10.1007/s12561-013-9081-1

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  • DOI: https://doi.org/10.1007/s12561-013-9081-1

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