Courses in Practical DNA Microarray Analysis 2004
November 22-25 in Berlin
Datasets and additional packages used in the practical sessions can be found in the data directory, links to the tutorial slides and practical exercises in the table below.
| Monday, Nov 22 - First Analysis steps | ||
| 09.00-09.30 | Introduction and overview | Benedikt Brors |
| 09.30-11.00 | cDNA chips: Quality control and preprocessing | Ulrich Mansmann |
| 11.15-12.15 | Affy Chips: Cel-file versus summary information | Ulrich Mansmann |
| 14.45-17.00 | Exercises: Introduction to R, cDNA data, affy data | Wolfgang Huber |
| Tuesday, Nov 23 - Exploratory analysis | ||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck |
| 10.30-12.00 | Clustering | Jörg Rahnenführer |
| 12.00-13.00 | Annotation | Benedikt Brors |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
v.Heydebreck Rahnenführer,Markowetz |
| Wednesday, Nov 24 - Molecular Diagnosis | ||
| 09.00-10.30 | Molecular Diagnosis | Rainer Spang |
| 10.30-11.30 | Classification by Nearest Shrunken Centroids and Support Vector Machines | Florian Markowetz |
| 11.30-12.30 | Model Assessment and Selection | Rainer Spang |
| 13.30-17.00 | Exercises: Molecular Diagnosis | Florian Markowetz |
| Thursday, Nov 25 - Pathways | ||
| 09.00-10.30 | Graphs and Networks in R | Wolfgang Huber |
| 10.30-11.30 | Structured Analysis of Microarrays Differential Coexpression |
Claudio Lottaz Rainer Spang |
| 11.30-12.30 | Group testing: global tests Scoring pathway activity |
Ulrich Mansmann Jörg Rahnenführer |
| 13.30-17.00 | Exercises: Group testing and time to work on your own data |
Ulrich Mansmann |
Background Knowledge
Ideally, you are interested in mathematical and statistical problems and are familiar with at least one programming language. This course focusses on the practical side of gene expression data analysis. However, data analysis without understanding the statistical background is in general impossible. We strongly recommend you to refresh your mathematical and programming skills before attending the course.
Please use the links to software and literature to prepare yourself before the course begins.
R and Bioconductor
In the afternoon exercises you will learn how to analyze data using the statistical computing environment R [http://www.r-project.org] and BioConductor [http://www.bioconductor.org], an open source software for bioinformatics. R sources and package sources can be downloaded from The Comprehensive R Archive Network at http://cran.r-project.org. Basics are explained in Introduction to R.
Bring your own data
You are encouraged to bring some of your own data to the course (e.g. genepix files or CEL/CDF). We will use this during the exercises. If you expect to have own data only later in the year, it may in fact be advantageous also to register for one of the later courses in Berlin or Heidelberg.
Participants
| • | Angelika Lüking | Ruhr Uni Bochum, Germany | |
| • | Ulrike Nuber | MPI Molecular Genetics Berlin, Germany | |
| • | Falk Hertwig | MPI Molecular Genetics Berlin, Germany | |
| • | Adriane Menssen | Charite Berlin, Germany | |
| • | Jochen Ringe | Charite Berlin, Germany | |
| • | Susana Kalko | Clinic Hospital Barcelona, Spain | |
| • | Matthew Hannah | MPI Molecular Plant Physiology Golm, Germany | |
| • | Justine Peeters | ErasmusMC Rotterdam, The Netherlands | |
| • | Elisabeth Lodder | ErasmusMC Rotterdam, The Netherlands | |
| • | Anand Gavai | Wageningen University, The Netherlands | |
| • | Florian Hahne | German Cancer Research Center, Heidelberg, Germany | |
| • | Dena Leshkowitz | Hebrew University, Israel | |
| • | Thorsten Rieck | RZPD Berlin, Germany | |
| • | Natalia Udilova | University of Veterinary Medicine Vienna, Austria | |
| • | K.Dayananda Rao | University of Köln, Germany | |
| • | Huamin Liang | University of Köln, Germany | |
| • | Bodo Brunner | Aventis GmbH, Frankfurt Main, Germany | |
| • | Hans-Christoph Schneider | Aventis GmbH, Frankfurt Main, Germany | |
| • | Uli Luxemburger | University of Mainz, Germany |
Thank you for registering! This course is fully booked and closed for registration. If you will not be able to attend, please contact Florian Markowetz as soon as possible so that we can notify the people on the waiting list.
Accomodation
We recommend rooms at the Hotel Ravenna in Berlin-Steglitz. Contact: http://www.ravenna-hotel.de.
How to find us
We meet at the Max-Planck-Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin-Dahlem, main building (Turm 2) third floor, big seminar room, on Mon Nov 22 at 9 am. The MPI-MG is next to the underground station Thielplatz (U1). Click here for detailed visitor informations.
Further information
Please contact Florian Markowetz: florian.markowetz@molgen.mpg.de.