This chapter discusses the analysis of microarray data derived from samples collected in clinical trials. Deoxyribonucleic acid (DNA) Microarray experiments are conducted in many areas of biomedical, biological, and biopharmaceutical research and development. Microarray techniques are applied to problems arising in gene discovery, diagnosis of disease, pharmacogenomics, and toxicogenomics among others. Microarrays are designed to simultaneously measure expression levels of thousands of genes in a particular tissue or disease cell type. There are several different microarray technologies, including the cDNA arrays developed at Stanford and the high density oligonucleotide arrays produced by Affymetrix. Along with the development of microarray technology, many new statistical methods and models have been developed in parallel and incorporated in software to analyze high-throughput data. The chapter introduces some basic concepts in bioinformatics specifically for gene, gene expression, and microarray. It uses data derived from breast cancer patients to illustrate the application of bioconductor with a step-by-step approach.