Practical DNA Microarray Analysis
Heidelberg 23.-27. September 2002Benedikt 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.