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Preface | p. xi |
Very Large Arrays | p. 1 |
Applications | p. 1 |
Problems | p. 2 |
Solutions | p. 2 |
Permutation Tests | p. 5 |
Two-Sample Comparison | p. 5 |
Blocks | p. 7 |
k-Sample Comparison | p. 8 |
Computing The p-Value | p. 9 |
Monte Carlo Method | p. 10 |
An R Program | p. 11 |
Multiple-Variable Comparisons | p. 11 |
Euclidean Distance Matrix Analysis | p. 12 |
Hotelling's T2 | p. 13 |
Mantel's U | p. 14 |
Combining Univariate Tests | p. 15 |
Gene Set Enrichment Analysis | p. 16 |
Categorical Data | p. 17 |
Software | p. 19 |
Summary | p. 20 |
Applying the Permutation Test | p. 23 |
Which Variables Should Be Included? | p. 24 |
Single-Value Test Statistics | p. 26 |
Categorical Data | p. 26 |
A Multivariate Comparison Based on a Summary Statistic | p. 26 |
A Multivariate Comparison Based on Variants of Hotelling's T 2 | p. 28 |
Adjusting for Covariates | p. 29 |
Pre-Post Comparisons | p. 31 |
Choosing a Statistic: Time-Course Microarrays | p. 32 |
Recommended Approaches | p. 35 |
To Learn More | p. 35 |
Biological Background | p. 37 |
Medical Imaging | p. 37 |
Ultrasound | p. 38 |
EEG/MEG | p. 39 |
Magnetic Resonance Imaging | p. 41 |
MRI | p. 41 |
fMRI | p. 42 |
Positron Emission Tomography | p. 44 |
Microarrays | p. 44 |
To Learn More | p. 47 |
Multiple Tests | p. 49 |
Reducing the Number of Hypotheses to Be Tested | p. 50 |
Normalization | p. 50 |
Selection Methods | p. 52 |
Univariate Statistics | p. 52 |
Which Statistic? | p. 54 |
Heuristic Methods | p. 55 |
Which Method? | p. 59 |
Controlling the Over All Error Rate | p. 59 |
An Example: Analyzing Data from Microarrays | p. 60 |
Controlling the False Discovery Rate | p. 61 |
An Example: Analyzing Time-Course Data from Microarrays | p. 62 |
Gene Set Enrichment Analysis | p. 63 |
Software for Performing Multiple Simultaneous Tests | p. 67 |
AFNI | p. 67 |
Cyber-T | p. 68 |
dChip | p. 68 |
ExactFDR | p. 69 |
GESS | p. 69 |
Haplo View | p. 69 |
MatLab | p. 69 |
R | p. 70 |
SAM | p. 70 |
ParaSam | p. 71 |
Summary | p. 72 |
To Learn More | p. 72 |
The Bootstrap | p. 73 |
Samples and Populations | p. 73 |
Precision of an Estimate | p. 74 |
R Code | p. 77 |
Applying the Bootstrap | p. 78 |
Bootstrap Reproducibility Index | p. 79 |
Estimation in Regression Models | p. 80 |
Confidence Intervals | p. 82 |
Testing for Equivalence | p. 83 |
Parametric Bootstrap | p. 84 |
Blocked Bootstrap | p. 85 |
Balanced Bootstrap | p. 85 |
Adjusted Bootstrap | p. 86 |
Which Test? | p. 87 |
Determining Sample Size | p. 88 |
Establish a Threshold | p. 89 |
Validation | p. 90 |
Cluster Analysis | p. 92 |
Correspondence Analysis | p. 94 |
Building a Model | p. 96 |
How Large Should The Samples Be? | p. 98 |
Summary | p. 99 |
To Learn More | p. 99 |
Classification Methods | p. 101 |
Nearest Neighbor Methods | p. 101 |
Discriminant Analysis | p. 102 |
Logistic Regression | p. 103 |
Principal Components | p. 103 |
Naive Bayes Classifier | p. 104 |
Heuristic Methods | p. 104 |
Decision Trees | p. 105 |
A Worked-Through Example | p. 106 |
To Learn More | p. 99 |
Which Algorithm Is Best for Your Application? | p. 108 |
Some Further Comparisons | p. 111 |
Validation Versus Cross-validation | p. 112 |
Improving Diagnostic Effectiveness | p. 113 |
Boosting | p. 113 |
Ensemble Methods | p. 113 |
Random Forests | p. 114 |
Software for Decision Trees | p. 116 |
Summary | p. 117 |
Applying Decision Trees | p. 119 |
Photographs | p. 119 |
Ultrasound | p. 121 |
MRI Images | p. 122 |
EEGs and EMGs | p. 124 |
Misclassification Costs | p. 125 |
Receiver Operating Characteristic | p. 126 |
When the Categories Are As Yet Undefined | p. 127 |
Unsupervised Principal Components Applied to fMRI | p. 127 |
Supervised Principal Components Applied to Microarrays | p. 129 |
Ensemble Methods | p. 131 |
Maximally Diversified Multiple Trees | p. 131 |
Putting It All Together | p. 133 |
Summary | p. 135 |
To Learn More | p. 135 |
Glossary of Biomedical Terminology | p. 137 |
Glossary of Statistical Terminology | p. 141 |
Appendix: An R Primer | p. 153 |
Getting Started | p. 153 |
R Functions | p. 155 |
Vector Arithmetic | p. 156 |
Store and Retrieve Data | p. 156 |
Storing and Retrieving Files from Within R | p. 156 |
The Tabular Format | p. 157 |
Comma Separated Format | p. 158 |
Resampling | p. 159 |
The While Command | p. 159 |
Expanding R's Capabilities | p. 161 |
Downloading Libraries of R Functions | p. 161 |
Programming Your Own Functions | p. 161 |
Bibliography | p. 165 |
Author Index | p. 175 |
Subject Index | p. 181 |
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