05484nam 22006494a 450 991084059230332120230617040820.01-282-30744-497866123074470-470-31712-40-470-31796-5(CKB)1000000000687577(EBL)468845(OCoLC)264621192(SSID)ssj0000337507(PQKBManifestationID)11297314(PQKBTitleCode)TC0000337507(PQKBWorkID)10294934(PQKB)10546657(MiAaPQ)EBC468845(EXLCZ)99100000000068757720030404d2004 uy 0engur|n|---|||||txtccrExploration and analysis of DNA microarray and protein array data[electronic resource] /Dhammika Amaratunga, Javier CabreraHoboken, NJ John Wileyc20041 online resource (270 p.)Wiley series in probability and statisticsDescription based upon print version of record.0-471-27398-8 Includes bibliographical references (p. 222-236) and indexes.Exploration and Analysis of DNA Microarray and Protein A rray Data; Contents; Preface; 1. A Brief Introduction; 1.1. A Note on Exploratory Data Analysis; 1.2. Computing Considerations and Software; 1.3. A Brief Outline of the Book; 2. Genomics Basics; 2.1. Genes; 2.2. DNA; 2.3. Gene Expression; 2.4. Hybridization Assays and Other Laboratory Techniques; 2.5. The Human Genome; 2.6. Genome Variations and Their Consequences; 2.7. Genomics; 2.8. The Role of Genomics in Pharmaceutical Research; 2.9. Proteins; 2.10. Bioinformatics; Supplementary Reading; Exercises; 3. Microarrays3.1. Types of Microarray Experiments3.1.1. Experiment Type 1: Tissue-Specific Gene Expression; 3.1.2. Experiment Type 2: Developmental Genetics; 3.1.3. Experiment Type 3: Genetic Diseases; 3.1.4. Experiment Type 4: Complex Diseases; 3.1.5. Experiment Type 5: Pharmacological Agents; 3.1.6. Experiment Type 6: Plant Breeding; 3.1.7. Experiment Type 7: Environmental Monitoring; 3.2. A Very Simple Hypothetical Microarray Experiment; 3.3. A Typical Microarray Experiment; 3.3.1. Microarray Preparation; 3.3.2. Sample Preparation; 3.3.3. The Hybridization Step; 3.3.4. Scanning the Microarray3.3.5. Interpreting the Scanned Image3.4. Multichannel cDNA Microarrays; 3.5. Oligonucleotide Arrays; 3.6. Bead-Based Arrays; 3.7. Confirmation of Microarray Results; Supplementary Reading and Electronic References; Exercises; 4. Processing the Scanned Image; 4.1. Converting the Scanned Image to the Spotted Image; 4.1.1. Gridding; 4.1.2. Segmentation; 4.1.3. Quantification; 4.2. Quality Assessment; 4.2.1. Visualizing the Spotted Image; 4.2.2. Numerical Evaluation of Array Quality; 4.2.3. Spatial Problems; 4.2.4. Spatial Randomness; 4.2.5. Quality Control of Arrays4.2.6. Assessment of Spot Quality4.3. Adjusting for Background; 4.3.1. Estimating the Background; 4.3.2. Adjusting for the Estimated Background; 4.4. Expression Level Calculation for Two-Channel cDNA Microarrays; 4.5. Expression Level Calculation for Oligonucleotide Arrays; 4.5.1. The Average Difference; 4.5.2. A Weighted Average Difference; 4.5.3. Perfect Matches Only; 4.5.4. Background Adjustment Approach; 4.5.5. Model-Based Approach; 4.5.6. Absent-Present Calls; Supplementary Reading; Exercises; 5. Preprocessing Microarray Data; 5.1. Logarithmic Transformation5.2. Variance Stabilizing Transformations5.3. Sources of Bias; 5.4. Normalization; 5.5. Intensity-Dependent Normalization; 5.5.1. Smooth Function Normalization; 5.5.2. Quantile Normalization; 5.5.3. Normalization of Oligonucleotide Arrays; 5.5.4. Normalization of Two-Channel Arrays; 5.5.5. Spatial Normalization; 5.5.6. Stagewise Normalization; 5.6. Judging the Success of a Normalization; 5.7. Outlier Identification; 5.7.1 Nonresistant Rules for Outlier Identification; 5.7.2. Resistant Rules for Outlier Identification; 5.8. Assessing Replicate Array Quality; Exercises; 6. Summarization6.1. ReplicationA cutting-edge guide to the analysis of DNA microarray data Genomics is one of the major scientific revolutions of this century, and the use of microarrays to rapidly analyze numerous DNA samples has enabled scientists to make sense of mountains of genomic data through statistical analysis. Today, microarrays are being used in biomedical research to study such vital areas as a drug's therapeutic value-or toxicity-and cancer-spreading patterns of gene activity. Exploration and Analysis of DNA Microarray and Protein Array Data answers the need for a comprehensive, cutting-edge overview of thWiley series in probability and statistics.DNA microarraysStatistical methodsProtein microarraysStatistical methodsDNA microarraysStatistical methods.Protein microarraysStatistical methods.572.8572.8636Amaratunga Dhammika1956-1667367Cabrera Javier614089MiAaPQMiAaPQMiAaPQBOOK9910840592303321Exploration and analysis of DNA microarray and protein array data4134529UNINA