Quality Control and Reproducibility in DNA Microarray Experiments

André Fujita[1] (andrefujita@riken.jp)
João Sato[2] (joao.sato@ufabc.edu.br)
Fernando H.L daSilva[3] (lojudice@iq.usp.br)
Maria C. Galvaõo[4] (mchrisgalvao@gmail.com)
Mari C.Sogayar[3] (mcsoga@iq.usp.br)
Satoru Miyano[1][5] (miyano@ims.u-tokyo.ac.jp)

[1] Computational Science Research Program, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
[2] Center of Mathematics, Computation and Cognition, Universidade Federal do ABC, Rua Satna Adélia, 166 - Santo André
[3] Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748 - São Paulo, 05508-000, Brazil
[4] Orthodontic Department, University Methodist of São Paulo, Rua Alfeu Tavares, 149 - São Bernardo do Campo, 09641-000, Brazil
[5] Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan


Biological experiments are usually set up in technical replicates (duplicates or triplicates) in order to ensure reproducibility and, to assess any significant error introduced during the experimental process. The first step in biological data analysis is to check the technical replicates and to confirm that the error of measure is small enough to be of no concern. However, little attention has been paid to this part of analysis. Here, we propose a general process to estimate the error of measure and consequently, to provide an interpretable and objective way to ensure the technical replicates' quality. Particularly, we illustrate our application in a DNA microarray dataset set up in technical duplicates.

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Japanese Society for Bioinformatics