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Table Of Contents

KLUWER ACADEMIC PUBLISHERS
2. BASIC BIOLOGY AND ARRAY PROTOCOL
2.1 Genes"R"us
2.2Brewing up the Hybridization Soup
2.4Into the Microarray Jungle
3. BASIC CONCEPTS OF MICROARRAY DATA ANALYSIS
4.DATA ANALYSIS = DATA + PROCESS
4.1Da Da Data
4.2 Process
3.EXPERIMENTAL DESIGN
5.5Alternative Approaches
8.CONCLUSIONS
9.REFERENCES
2. ALGORITHMS
2.1KNNimpute Algorithm
2. NORMALIZATION METHODS
2.2 Regression Methods
2.4 Summary
2.1Visualization of the SVD
2.3Examples from the literature
4.FURTHER READING AND RESOURCES
2.3The ORDERED-FS Algorithm
3. FEATURE WEIGHTING
3.1The WINNOW Algorithm
3.2Bayesian Feature Selection
4.3The CLICK Algorithm
1.1Motivation: Tumor Classification Using Gene Expression Data
1.2 Outline
2.STATISTICAL FOUNDATIONS OF CLASSIFICATION
2.1Background on Classification
3.BASIC CLASSIFIERS
3.1Linear and Quadratic Discriminant Analysis
3.2Nearest Neighbor Classifiers
5. PERFORMANCE ASSESSMENT
5.1Resubstitution Estimation
5.2Test Set Estimation
5.4General Issues in Performance Assessment
6. DISCUSSION
3.1Discretization and Selection
3.2 Learning Bayesian Networks from Data
4.2Difficulties in Using Bayesian Networks for Classification
4.3Improving the Classification Accuracy of the Bayesian Network
5.1The Microarray Data Sets
5.3Experimental Results
6.CONCLUDING REMARKS
ACKNOWLEDGMENTS
2.SUPPORT VECTOR MACHINES
2.2An Application ofSVMs
3.GENE SELECTION
3.1Signal-to-Noise (S2N)
3.2Recursive Feature Elimination (RFE)
3.3How Many Genes To Use?
4.ERROR RATES FOR MORPHOLOGY AND TREATMENT OUTCOME PREDICTION
7.DISCUSSION
2.4Permutation t-Test
3.3Leave-One-Out Cross-Validated Class Prediction Model
3.1ANN Architecture
3.2Training the ANN
3.4Random Permutation Tests
4.IMPLEMENTATION
5.SUMMARY
1.3Why a Genetic Algorithm?
2.THE GA/KNN METHOD
2.1Overall Methodology
2.2KNN
2.3A Genetic Algorithm
ACKNOWLEDGEMENTS
2. DESIGN PRINCIPLES FOR CLUSTERING
2.2Basic Criteria For The Selection Of Clustering
3.1Assessing Cluster Quality With Dunn’s Validity Indices
4.CONCLUSIONS
3. HIERARCHICAL CLUSTERING METHODS
4. EXAMPLES
4.1 Simulated Data
4.2 Lymphoma Data
2.1 The SOM Clustering Algorithm
Data
3.SIMILARITY METRICS
4.CLUSTERING ALGORITHMS
4.1 CAST
4.2K-means
4.3 PAM
5.ASSESSMENT OF CLUSTER QUALITY
5.2Internal Validation
6. MODEL-BASED APPROACH
6.1 The Model-based Framework
6.2 Algorithm Outline
6.3 Model Selection
6.4Implementation
7.A CASE STUDY
2.TYPES OF VARIABLES
3.MEASUREMENT AND TEST OF CORRELATION
3.1Pearson’s Product-Moment Correlation Coefficient
3.2Spearman’s Rank-Order Correlation Coefficient
3.3Kendall’s Tau
3.4Comparison of Different Correlation Coefficients
3.5Pearson’s Contingency Coefficient
3.6Statistical Tests of Correlation
4.MINING ASSOCIATION RULES
4.1Association Rules
4.2Machine Learning Algorithms for Mining Association
5. CAUSATION AND ASSOCIATION
6.APPLICATIONS IN MICROARRAY STUDIES
6.1Using Correlation Coefficients for Clustering
6.2Associating Profiles, or Associating Genes with Drug
6.3Inferring Genetic Networks
6.4 Mining Association Rules from Genomic Data
6.5 Assessing the Reliability and Validity of High-
6.6 Conclusions
RESEARCH
EXPRESS
3.1 Statistical Approaches
4.DISCUSSION
4.1 Utility, Need, and Impact
4.2 Other Related Work and Resources
2. PRIMER/PROBE DESIGN SOFTWARE
3. IMAGE ANALYSIS SOFTWARE
5.1R Packages for Microarray Analysis
3.1Business Understanding
3.3Data Preparation
3.5 Evaluationof Project Results
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A Practical Approach to Microarray Data Analysis-Daniel P. Berrar

A Practical Approach to Microarray Data Analysis-Daniel P. Berrar

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Published by: Bashistha Kanth on Mar 01, 2011
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