[StATS]: Permutation tests for microarrays (July 27, 2005).
A very simple approach to estimating the proportion of differentially expressed genes uses a permutation approach. The reference for this is
- Empirical Bayes Analysis of a Microarray Experiment. Efron B, Tibshirani R, Storey JD, Tusher V. Journal of the American Statistical Association 2001: 96(456); 1151-1160. [PDF]
Several related articles discuss how to use permutation tests to estimate the positive false discovery rate:
- Statistical significance for genomewide studies. Storey JD, Tibshirani R. Proc Natl Acad Sci U S A 2003: 100(16); 9440-5. [Medline] [Abstract] [Full text] [PDF]
- A direct approach to false discovery rates. Storey JD. J. R. Statist. Soc. B 2002: 64(Part 3); 479-498. [PDF]
- The Positive False Discovery Rate: A Bayesian Interpretation and the q-Value. Storey JD. The Annals of Statistics 2003: 31(6); 2013-2035. [PDF]
- Identifying differentially expressed genes using false discovery rate controlling procedures. Reiner A, Yekutieli D, Benjamini Y. Bioinformatics 2003: 19(3); 368-75. [Medline] [Abstract] [PDF]
- Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. Storey JD, Taylor JE, Siegmund D. J. R. Statist. Soc. B 2004: 66(Part 1); 187-205. [PDF]
- Empirical bayes methods and false discovery rates for microarrays. Efron B, Tibshirani R. Genet Epidemiol 2002: 23(1); 70-86. [Medline] [PDF]
When I have time, I’ll show a simple example of this.
You can find an earlier version of this page on my website.