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Informationen zum Autor Steen Knudsen received his Ph.D. from the University of Copenhagen in 1990 and was among the pioneers of bioinformatics with a publication in Nature the same year. His postdoctoral training in bioinformatics at Harvard University concerned computational gene finding in the human genome. Since 1998 he has been working with methods for analysis of DNA microarray data. He currently heads the DNA microarray group at the Technical University of Denmark. Klappentext Written for biologists and medical researchers who don't have any special training in data analysis and statistics, Guide to Analysis of DNA Microarray Data, Second Edition begins where DNA array equipment leaves off: the image produced by the microarray. The text deals with the questions that arise starting at this point, providing an introduction to microarray technology, then moving on to image analysis, data analysis, cluster analysis, and beyond. With all chapters rewritten, updated, and expanded to include the latest generation of technology and methods, Guide to Analysis of DNA Microarray Data, Second Edition offers practitioners reliable information using concrete examples and a clear, comprehensible style. This Second Edition features entirely new chapters on: * Image analysis * Experiment design * Automated analysis, integrated analysis, and systems biology * Interpretation of results Intended for readers seeking practical applications, this text covers a broad spectrum of proven approaches in this rapidly growing technology. Additional features include further reading suggestions for each chapter, as well as a thorough review of available analysis software. Zusammenfassung Written for biologists and medical researchers who don't have any special training in data analysis and statistics, this text provides an introduction to microarray technology, and then moves on to image analysis, data analysis, cluster analysis, and beyond. Inhaltsverzeichnis Preface. Acknowledgments. 1. Introduction to DNA Microarray Technology. 1.1 Hybridization. 1.2 Gold Rush? 1.3 The Technology behind DNA Microarrays. 1.3.1 Affymetrix GeneChip Technology. 1.3.2 Spotted Arrays. 1.3.3 Digital Micromirror Arrays. 1.3.4 Inkjet Arrays. 1.3.5 Bead Arrays. 1.3.6 Serial Analysis of Gene Expression (SAGE). 1.4 Parallel Sequencing on Microbead Arrays. 1.4.1 Emerging Technologies 1.5 Example: Affymetrix vs. Spotted Arrays. 1.6 Summary. 1.7 Further Reading. 2. Overview of Data Analysis. 3. Image Analysis. 3.1 Gridding. 3.2 Segmentation. 3.3 Intensity Extraction. 3.4 Background Correction. 3.5 Software. 3.5.1 Free Software for Array Image Analysis. 3.5.2 Commercial Software for Array Image Analysis. 3.6 Summary. 3.7 Further Reading. 4. Basic Data Analysis. 4.1 Normalization. 4.1.1 One or More Genes are Assumed Expressed at Constant Rate. 4.1.2 Sum of Genes is Assumed Constant. 4.1.3 Subset of Genes is Assumed Constant. 4.1.4 Majority of Genes Assumed Constant. 4.1.5 Spike Controls. 4.2 Dye Bias, Spatial Bias, Print Tip Bias. 4.3 Expression Indices. 4.3.1 Average Difference. 4.3.2 Signal. 4.3.3 Model-Based Expression Index. 4.3.4 Robust Multiarray Average. 4.3.5 Position Dependent Nearest Neighbor Model. 4.4 Detection of Outliers. 4.5 Fold Change. 4.6 Significance. 4.6.1 Multiple Conditions. 4.6.2 Nonparametric Tests. 4.6.3 Correction for Multiple Testing. 4.6.4 Example I: t -Test and ANOVA. 4.6.5 Example II: Number of Replicates. 4.7 Mixed Cell Populations. 4.8 Summary. 4.9 Further Reading. 5. Visualization by Reduction of Dimension...
