Courses in Practical DNA Microarray Analysis 2004
March 08 - 11 in Heidelberg
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.
And here are some pictures to prove that microarray analysis can be a lot of fun.
| Monday, March 08 | ||
| 09.00-10.30 | First analysis steps | Wolfgang Huber |
| 11.00-12.30 | Differential gene expression | Anja von Heydebreck |
| 13.30-14.30 | First steps in R | Florian Markowetz |
| 14.45-17.00 | Exercises: Exploring cDNA data | Wolfgang Huber |
| Tuesday, March 09 | ||
| 09.00-10.30 | Exploratory data analysis | Jörg Rahnenführer |
| 10.30-11.30 | Resampling and the bootstrap | Axel Benner |
| 11.30-12.00 | Screening by ROC curve analysis | Axel Benner |
| 13.30-14.30 | BioConductor | Wolfgang Huber |
| 14.45-17.00 | Exercises: 2x2 factorial design | Wolfgang Huber |
| Wednesday, March 10 | ||
| 09.00-11.00 | Design of microarray experiments | Ulrich Mansmann |
| 11.00-12.30 | Annotation | Benedikt Brors |
| 13.30-17.00 | Exercises: Experimental Design | Ulrich Mansmann |
| Thursday, March 11 | ||
| 09.00-10.30 | Molecular Diagnosis | Rainer Spang |
| 10.30-11.30 | Classification by Support Vector Machines | Florian Markowetz |
| 11.30-12.30 | Model Assessment and Selection | Axel Benner |
| 13.30-17.00 | Exercises: classification, model selection | Florian Markowetz Axel Benner |
How to find us
We will meet on the science campus of the university of Heidelberg, "Im Neuenheimer Feld", building no. 305, room 144 (that is the seminar room on the 1st floor) on Monday March 08 at 9 am.
Here are some links that may be helpful in finding the Neuenheimer Feld in Heidelberg:
http://www.uni-heidelberg.de/univ/besucher/anfahrt.html
http://med.uni-hd.de/karte/index.html
And here is a map that should help you in finding building 305 - it is marked with a circle:
http://www.uni-heidelberg.de/univ/besucher/karten/6305.html
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.
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.
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], a 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.
Participants
| • | Benjamin Haibe-Kains | Jules Bordet Hospital and Free University of Brussels, Belgium. | |
| • | Barbara Vollmayr | Mannheim, Germany. | |
| • | Georg Wilhelm Otto | Max-Planck-Institute for Developmental Biology, Tuebingen, Germany. | |
| • | Luzie U. Wingen | Institut fuer Zell- und Molekularpathologie, Medizinische Hochschule Hannover, Germany. | |
| • | Stefan Berger | Department of Molecular Biology, Central Institute of Mental Health, Mannheim, Germany. | |
| • | Eric Cabannes | Laboratoire d'Immunologie Virale, Institut Pasteur, Paris, France. | |
| • | Lysiane Laurent | Laboratoire d'Immunologie Virale, Institut Pasteur, Paris, France. | |
| • | Axel Weber | Institut für Pharmakologie, Medizinische Hochschule Hannover, Germany. | |
| • | Oliver Dittrich | Institut für Pharmakologie, Medizinische Hochschule Hannover, Germany. | |
| • | Anja Matthaei | Inst. Med. Genetik, Tumorgenetik, Campus Virchow Klinikum, Berlin, Germany. | |
| • | Eva Klopocki | Inst. Med. Genetik, Tumorgenetik, Campus Virchow Klinikum, Berlin, Germany. | |
| • | Stana Radic | Department of Physics, University of Cologne, Germany. | |
| • | Floor Stam | Vrije Universiteit Amsterdam, Molecular and Cellular Neurobiology, Amsterdam, Netherlands | |
| • | Roel Verhaak | Erasmus Medical Center, Rotterdam, Netherlands. | |
| • | Karin Lemuth | Univ. Stuttgart, Germany. | |
| • | Anissa Boucherot | Klinische Biochemie, Medizinische Poliklinik der LMU München. | |
| • | Michael Moorhouse | Rotterdam, Netherlands. | |
| • | Jean-Francois Laes | Jules Bordet Institute, Brussels, Belgium. |
Thank you for registering! This course is fully booked and closed for registration. If you will not be able to attend, please contact Wolfgang Huber as soon as possible so that we can notify the people on the waiting list.
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 Dr. Wolfgang Huber: w.huber@dkfz.de