Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition

Chapter 21

Methods for selecting differentially

expressed genes

Everything should be made as simple as possible, but not simpler.

—Albert Einstein

21.1 Introduction

In many cases, the purpose of the micr oarray experiment is to c ompare the

gene expression levels between two different phenotypes.

1

In most cases, one

sample is c onsidered the reference or control and the other one is considered

the experiment. Obvious exa mples include compa ring healthy versus dis ease,

treated versus untreated, drug A versus drug B, before and after treatment,

etc. Sample comparison may be done using different arrays (e.g., oligonu-

cleotide arrays) or multiple channels