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

Chapter 5

Image processing

Not everything that can be counted counts, and not everything that cou nts

can be counted.

—Albert Einstein

5.1 Introduction

The main goal of array image processing is to measure the intensity of the

spots and quantify the gene expression values based on these intensities. A

very important and often neglected goal is also assessing the reliability of

the data, and generating warnings signaling possible problems during the ar-

ray production and/ or hybridization phases. This chapter is divided into two

parts. Section 5.2 provides a very short description of the basic notio ns in-

volved in digital imaging. Section 5.3 and follo ...