Computation in BioInformatics

8DNA Microarray Analysis: From Affymetrix CEL Files to Comparative Gene Expression

Sandeep Kumar¹*, Shruti Shandilya², Suman Kapila³, Mohit Sharma^4,5 and Nikhil Agrawal^6†

¹International Institute of Veterinary Education & Research, Haryana, Rohtak, India

²Department of Applied Physics, Aalto University, Espoo, Finland

³ICAR-National Dairy Research Institute, Haryana, India

⁴Post Graduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland

⁵Malopolskie Centre of Biotechnology, Jagiellonian University, Krakow, Poland

⁶College of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa

Abstract

Microarray technique is widely used for the rapid detection and comparison of expression of thousands of genes at the same time. For the microarray data analysis, robust and reproducible protocols are being generated day by day. Bioconductor provides several free microarray data analysis packages. The analysis includes the following processes: quality control, normalization, and calculation of differential gene expression. This chapter demonstrates a protocol to find out the differentially expressed genes from the raw data (.CEL files) using the Bioconductor tools.

Keywords: Microarray, bioconductor, genes

8.1 Introduction

DNA microarray, also known as DNA chip, is a molecular technique used to quantify mRNA expression in the cells/tissues [1]. In this technique, an array of hundreds of known DNA fragments called as probes is immobilized on ...