Significance Testing of Microarray Data
BIOS 691-803; Spring 2010
Instructor: Dr. Mark Reimers, VCU
Anthony Davison's slides
Anya von Heydebreck's slides
NB. Papers marked with a P may be presented by students.
Bretz et al give a concise overview of the issues in multiple testing.
Reiner sketches out the Benjamini-Hochberg approach to FDR.
The original Benjamini & Hochberg paper proving their theorem about FDR.
Storey defines a related but different FDR and gives it a Bayesian interpretation. P
Korn et al. show how to use permutations to get upper bounds on actual FDR. P
Smythe derives an empirical Bayes approach to expression testing. P
David Allison does a comparison of how different FDR methods do in practice.
Try out this script to explore the relation between true and false positives.
Try out this script to explore the relation between true and false positives using the Benjamini-Hochberg approach.
Test the performance and variability of the SAM (use BioC's siggenes) and limma procedures under various correlation regimes.
First construct data that is independent; then construct tests that are positively correlated and finally tests that are both positively and negatively correlated.
Here are the limma and siggenes guides.