This is the first edition of the DNA microarray data analysis guidebook. Although invented in themid-90s, DNA microarrays are still novelties as biomedical research tools. DNA microarrays generate large amounts of numerical data, which should be analyzed effectively. In this book, we hope to offer a broad view of basic theory and techniques behind the DNA microarray data analysis. Our aim was not to be comprehensive, but rather to cover the basics, which are unlikely to change much over years. We hope that especially researchers starting their data analysis can benefit from the book.
The text emphasizes gene expression analysis. Topics, such as genotyping, are discussed shortly. This book does not cover the wet-lab practises, such as sample preparation or hybridization. Rather, we start when the microarrays have been scanned, and the resulting images analyzed. In other words, we take the files with signal intensities, which usually generate questions such as: “How is the data normalized?” or “How do I identify the genes which are upregulated?”. We provide some simple solutions to these specific questions and many others.

 

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