Genomics Data Analysis-False Discovery Rates and Empirical Bayes Methods

1. Basic probability and statistics 
Biological background
Probability distributions 
Probability functions
Contingency tables 
Hypothesis tests and p values 
Bibliographical notes
Exercises (PS1-PS3)
2. Introduction to likelihood 
Likelihood function defined 
Odds and probability: What’s the difference?
Bayesian uses of likelihood 
Bibliographical notes 
Exercises (L1-L3) 
3. False discovery rates 
Introduction 
Local false discovery rate 
Global and local false discovery rates 
Computing the LFDR estimate 
Bibliographical notes
Exercises (L4; A-B)
4. Simulating and analyzing gene expression data 
Simulating gene expression with dice 
DE games
Effects and Estimates (E&E)
Under the hood: normal distributions 
Bibliographical notes 
Exercises (C-E; G1-G4) 
5. Variations in dimension and data 
Introduction
High-dimensional genetics 
Subclasses and superclasses 
Medium number of features
Bibliographical notes
Exercise (G5) 
6. Correcting bias in estimates of the false discovery rate 
Why correct the bias in estimates of the false discovery rate? 
A misleading estimator of the false discovery rate 66
Corrected and re-ranked estimators of the local false discovery rate 
Application to gene expression data analysis
Bibliographical notes 
Exercises (CFDR0-CFDR3) 
7. The L value: An estimated local false discovery rate to replace a p value 
What if I only have one p value? Am I doomed?
The L value to the rescue! 
The multiple-test L value
Bibliographical notes 
Exercises (LV1-LV9)
8. Maximum likelihood and applications 
Non-Bayesian uses of likelihood 
Empirical Bayes uses of likelihood 
Bibliographical notes 
Exercises (M1-M2) 
Appendix A. Generalized Bonferroni correction derived from conditional compatibility
A non-Bayesian approach to testing single and multiple hypotheses
Bibliographical notes 
Appendix B. How to choose a method of hypothesis testing 
Guidelines for scientists performing statistical hypothesis tests 
Bibliographical notes 
Appendix. Bibliography