Significance Testing of Microarray Data

BIOS 691-803; Spring 2010

Instructor: Dr. Mark Reimers, VCU

#### Slides

My slides

Anthony Davison's slides

Anya von Heydebreck's slides

#### Papers

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.

#### Exercises

Try out this script to explore the relation between true and false positives.
#### Homework

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.