Courses in Practical DNA Microarray Analysis 2005
2005 March 14-17 in Heidelberg
| Monday, Mar 14 - 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 | Tresch, Buness, Beissbarth, Huber |
| Tuesday, Mar 15 - 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, Mar 16 - 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, Mar 17 - Pathways | ||
| 09.00-10.30 | Graphs and Networks in R | Wolfgang Huber |
| 10.30-11.30 | Structured Analysis of Microarrays Differential Coexpression |
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.
This is a course in microarray analysis -- not an introduction to R. Please read the Introduction to R before the course begins.
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.
Participants
| • | Jörn Kamradt | Universitätsklinikum des Saarlandes, Homburg, Germany | |
| • | Annegret Fischer | University of Munich, Germany | |
| • | Manon von Bülow | Aventis Pharma Deutschland GmbH, Frankfurt, Germany | |
| • | Henning Redestig | MPI for Molecular Plant Physiology, Golm, Germany | |
| • | Claudia Döring | University of Frankfurt, Germany | |
| • | Anand Gavai | University of Wageningen, The Netherlands | |
| • | Pie Müller | Liverpool School of Tropical Medicine, UK | |
| • | Clare Strode | Liverpool School of Tropical Medicine, UK | |
| • | Fernando Leonardi | Zentralinstitut für Seelische Gesundheit, Mannheim | |
| • | Almut Nitsche | Sanofi-Aventis, Functional Genomics, Frankfurt, Germany | |
| • | Eli Reuveni | EMBL Monterotondo, Italy | |
| • | Nancy Mah | Institute of Clinical Molecular Biology, University of Kiel, Germany | |
| • | Matjaz Hren | National Institute of Biology, Department of Plant Physiology and Biotechnology, Ljubljana, Slovenia | |
| • | Kristina Gruden | National Institute of Biology, Department of Plant Physiology and Biotechnology, Ljubljana, Slovenia | |
| • | Victor de Jager | Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands | |
| • | Matteo Pardo | Sensor Lab, INFM-CNR, Brescia, Italy |
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.
How to find us
We meet Monday, March 14, at 9am in the German Cancer Research Center (DKFZ) main building, room H824 (8. floor). The DKFZ lies on the science campus of the university of Heidelberg, "Im Neuenheimer Feld", building 280.
This document may be helpful in finding the Neuenheimer Feld in Heidelberg: anfahrt_dkfz.pdf. Unfortunately it is in German only, but contains a number of very detailed maps guiding you to the DKFZ (INF 280).
Accomodation
You will need to make your own accommodation arrangements.
• The most useful website for this is the Heidelberg tourist information: http://www.cvb-heidelberg.de.
• The IBIS hotel is a generic budget hotel, close to the train station, and in walking distance from the course venue and from downtown: http://www.ibishotel.com.
• The hotel Frisch is right next to the university campus: http://www.cafe-frisch.de.
Further information
Please contact Florian Markowetz: florian.markowetz@molgen.mpg.de.