DNA microarrays and related genomics techniques : designs, analysis, and interpretation of experiments /: designs, analysis, and interpretation of experiments. (2006)

• Record Type: Book
• Further Information: Note: Edited by David B. Allison [and others].
• Other Names: Allison, David B (David Bradley), 1963-
• Contents: Microarray Platforms and Blood Samples, P.M. Gaffney, K.L. Moser, E.C. Baechler, and T.W. Behrens ; Introduction; Microarray Technology; Autoantigen and Cytokine Microarrays; DNA and Oligonucleotide Microarrays; Tiling Arrays; Data Analysis; Future Directions; References; Normalization of Microarray Data, R.S. Parrish and R.R. Delongchamp ; Objectives of Normalization; Statistical Basis of Normalization; Normalization Algorithms; Evaluating Normalization Methods; References; Microarray Quality Control and Assessment, D. Finkelstein, M. Janis, A. Williams, K. Steiger, and J. Retief ; Introduction; Array Quality and Qesign; Bioinformatic Quality; Manufacturing Quality; Experimental Design Quality; Experimenatal Execution; Quality Control Metrics; Data Analysis Quality; Quality of Interpretation; Quality of Validation; Making Decisions Based on Quality; Conclusions; References; Epistemological Foundations of Statistical Methods for High-Dimensional Biology, S.O. Zakharkin, T. Mehta, M. Tanik, and D.B. Allison ; The Challenge We Face; Our Vantage Point: From Samples to Populations; What is Validity?; Comparison of Different Methods; Data Sets of Unknown Nature: Circular Reasoning; The Search for Proof: Deduction; The Proof of the Pudding is in the Eating: Induction; Combined Modes; Where to from Here?; Acknowledgments; References; The Role of Sample Size on Measures of Uncertainty and Power, G.L. Gadbury, Q. Xiang, J. Edwards, G.P. Page, and D.B. Allison ; Introduction; TP, TN, and EDR in Microarray Experiments; Sample Size and Sources of Uncertainty in Microarray Studies; On the Distribution of p-Values; A Mixture Model for the Distribution of p-Values; Planning Future Experiments: The Role of Sample Size on TP, TN, and EDR; Sample Size and Threshold Selection: Illustrating the Procedure; Discussion; Acknowledgements; References; Pooling Biological Samples in Microarray Experiments, C.M. Kendziorski ; Introduction; Derivation of the Analogous Formula; Assumptions Used to Derive the Formula 9; Utility of Pooling; Conclusion; Designing Microarrays for the Analysis of Gene Expressions, J.Y. Chang and J.C. Hsu ; Two Approaches to Gene Expressions Analysis; Designing 2-Channel Microarrays; Modeling 2-Channel Microarray Gene Expression Data; Estimation When the Microarray design is not Orthogonal; Summary; References; Overview of Standard Clustering Approaches for Gene ; Microarray Data Analysis, E. Garrett-Mayer ; Introduction; Distance and Similarity Measures; Hierarchical Clustering; K-means and K-medoids; Self-Organizing Maps; Cluster Affinity Search Technique; Other Related Methods; Assessing Cluster Fit and Choosing K; Choosing Genes and Samples for Clustering Cluster Stability, B.S. Gorman and K. Zhang ; Cluster Stability; Defining Stability; A Brief Overview of Clustering; Choice Points that Influence Stability and Instability; A General Approach for Detecting Stable Cluster Solutions; References; Dimensionality Reduction and Discrimination, J. Kowalski and Z. Zhang ; Introduction; Dimension Reduction; Discrimination; Conclusion; References; Modeling Affymetrix Data at the Probe Level, T.-M. Chu, S. Deng, and R.D. Wolfinger ; Introduction; Models; The Primate Example; Simulation Study; Discussion; References Parametric Linear Models, C.S. Coffey and S.S. Cofield ; Introduction; Existing Methods for Two-Group Comparisons; Existing Methods for Linear Models; A Comparison of the Methods; Summary; References; The Use of Nonparametric Procedures in the Statistical Analysis of Microarray Data, T.M. Beasley, J.P.L. Brand, and J.D. Long ; Introduction; Motivating Example; Nonparametric Bootstrap; Permutation-Based Nonparametric Methods; Chebby Checker Methods; Discussion; Bayesian Analysis of Microarray Data, J.W. Edwards and P. Ghosh ; Introduction; Probability of True Differential Expression; Estimating the Null Distribution; Estimating the Evidence; Estimating the Prior Probability of Nondifferential Expression; Hierarchical Models; References; False Discovery Rate and Multiple Comparison Procedures, C. Sabatti ; Multiple Comparison in Microarrays; Multiple Testing; Simultaneous Inference — Beyond Testing; References; Using Standards to Facilitate Interoperation of Heterogeneous Microarray Databases and Analytic Tools, K.-H. Cheung ; Introduction; Using Standards to Tackle the Heterogeneity Problem; Future directions; Acknowledgements; References; Postanalysis Interpretation: “What Do I Do With this ; Gene List?” M.V. Osier ; Introduction; Overview of Current Methods; Knowledgebase Approaches; Supplementary Data Approaches; Tentative Function Assignment Approaches; Future Directions; Conclusions; Acknowledgements; References; Combining High Dimensional Biological Data to Study Complex Diseases and Quantitative Traits, G.P. Page and D.M. Ruden ; Introduction; Heritable Changes in Gene Expression; Combined HDB Techniques to Identify Candidate or Causal Genes for Complex Diseases and Quantitative Traits; Theoretical Papers; Software and Bioinformatics Tools; Issues With Combined High Dimensional Biological Projects; Conclusions about Combined HDB Studies; References
• Publisher Details: Boca Raton : Chapman & Hall/CRC
• Publication Date: 2006
• Extent: 1 online resource (371 pages), illustrations
• Subjects: 572.8/636; DNA microarrays; Oligonucleotide Array Sequence Analysis -- methods; Genetic Techniques; SCIENCE -- Life Sciences -- Genetics & Genomics; DNA microarrays; Electronic books
• Languages: English
• ISBNs: 1420028790; 9781420028799
• Related ISBNs: 0824754611
• Notes: Note: Includes bibliographical references and index.; Note: Print version record.
• Access Rights: Legal Deposit; Only available on premises controlled by the deposit library and to one user at any one time; The Legal Deposit Libraries (Non-Print Works) Regulations (UK).
• Access Usage: Restricted: Printing from this resource is governed by The Legal Deposit Libraries (Non-Print Works) Regulations (UK) and UK copyright law currently in force.