Practical DNA Microarray Analysis

Heidelberg 23.-27. September 2002
Benedikt Brors1, Anja von Heydebreck2, Wolfgang Huber3, Ulrich Mansmann4, Florian Markowetz2, Rainer Spang2

1German Cancer Research Center, Heidelberg, Dep. Intelligent Bioinformatics Systems;
2Max-Planck-Institute for Molecular Genetics, Berlin, Dep. Computational Molecular Biology;
3German Cancer Research Center, Heidelberg, Dep. Molecular Genome Analysis;
4Univ. of Heidelberg, Institute for Medical Biometry;

Schedule

Monday
9.00-10.30 DNA microarray technology and experiments (pdf)
11.00-12.30 Design of microarray experiments (part 1 pdf, part 2 pdf)
13.30-14.30 Introduction to R (ppt, pdf)
14.45-17.00 Practical exercises: data handling, exploration; normalization, testing
(pdf, solutions pdf, data tar.gz, Rnw, Sweave script)
Tuesday
9.00-10.30 Resampling and bootstrapping (pdf)
11.00-12.30 Multiple testing: (pdf)
13.30-14.30 Introduction to Bioconductor (ppt, pdf)
14.45-17.00 Practical exercises (ctd. from Monday)
Wednesday
9.00-11.15 First steps: Quality control, calibration, data transformation (ppt, pdf)
11.45-12.30 Annotation (pdf)
13.30-17.00 Practical exercises (ctd. from Monday)
Thursday
9.00-11.00 Molecular Diagnosis (pdf, ppt)
11.30-12.30 Classification by support vector machines (pdf)
13.30-17.00 Practical exercises (pdf, data zip)
Friday
9.00-10.30 Exploratory methods (pdf)
11.45-12.30 Software demo: Cluster/Treeview, GeneCluster, TIGR
13.30-17.00 Practical exercises (working with own data)

Course format

ca. 15 students from laboratories that work with microarrays. In the mornings, theory lectures; in the afternoons, hands-on-experience in computer-classes with real data sets (public data, or students' own data), using R/Bioconductor.

Fred Hutchinson Cancer Research Center