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Microarray Data Preprocessing: From Experimental Design to Differential Analysis

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Microarray Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2401))

Abstract

DNA microarray data preprocessing is of utmost importance in the analytical path starting from the experimental design and leading to a reliable biological interpretation. In fact, when all relevant aspects regarding the experimental plan have been considered, the following steps from data quality check to differential analysis will lead to robust, trustworthy results. In this chapter, all the relevant aspects and considerations about microarray preprocessing will be discussed. Preprocessing steps are organized in an orderly manner, from experimental design to quality check and batch effect removal, including the most common visualization methods. Furthermore, we will discuss data representation and differential testing methods with a focus on the most common microarray technologies, such as gene expression and DNA methylation.

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Authors and Affiliations

  1. Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland

    Antonio Federico, Laura Aliisa Saarimäki, Angela Serra, Giusy del Giudice, Pia Anneli Sofia Kinaret & Dario Greco

  2. BioMediTech Institute, Tampere University, Tampere, Finland

    Antonio Federico, Laura Aliisa Saarimäki, Angela Serra, Giusy del Giudice, Pia Anneli Sofia Kinaret & Dario Greco

  3. Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Tampere University, Tampere, Finland

    Antonio Federico, Laura Aliisa Saarimäki, Angela Serra, Giusy del Giudice, Pia Anneli Sofia Kinaret & Dario Greco

  4. Institute of Biotechnology,, University of Helsinki, Helsinki, Finland

    Pia Anneli Sofia Kinaret & Dario Greco

  5. Department of Biology, University of Naples Federico II, Naples, Italy

    Giovanni Scala

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  1. Antonio Federico
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  2. Laura Aliisa Saarimäki
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  3. Angela Serra
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  4. Giusy del Giudice
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  6. Giovanni Scala
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  7. Dario Greco
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Correspondence to Dario Greco .

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Editors and Affiliations

  1. Dipartimento di Giurisprudenza, Economia e Sociologia, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy

    Giuseppe Agapito

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Federico, A. et al. (2022). Microarray Data Preprocessing: From Experimental Design to Differential Analysis. In: Agapito, G. (eds) Microarray Data Analysis. Methods in Molecular Biology, vol 2401. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1839-4_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1839-4_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1838-7

  • Online ISBN: 978-1-0716-1839-4

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