Statistics for Bioinformatics

Lectures

  1. Slides
  2. Suggested reading
  3. Links

Practicals

  1. Introduction

Settings

  1. Configuration
  2. R librairies

Statistical analysis with R

  1. Basic operations
  2. The normal distribution
  3. Sampling distributions
  4. Student conformity test

Motif occurrences

  1. Word probabilities
  2. Testing mulptile words
  3. Applying alternative distributions
  4. Fitting a distribution

Microarray data analysis

  1. Introduction
  2. Fitting
  3. Standardization
  4. Single-chip significance testing
  5. Standardizing many chips
  6. Student multi-tests
  7. Clustering with R
  8. Supervised classification
  9. Case study: Berry et al. (2010)

ASG1 - 2012

  1. Intro to Unix (slides)
  2. TD: Handling genome coordinates
  3. TD: GO statistics
  4. Affymetrix normalization (slides)
  5. TD: A quick tutorial to the R langage
  6. TD: Handling and normalizing affymetrix data with bioconductor
  7. TD: Selecting differentially expressed genes with R or TmeV
  8. Sampling distributions
  9. Multiple testing corrections
  10. Supervised classification
  11. RNA-seq Introduction
  12. RNA-seq practical session

Course material

  1. R files
  2. Datasets

Contact

Jacques van Helden
jacques.van-helden@univ-amu.fr

Aug 2002 - Oct 2008