Courses in Practical DNA Microarray Analysis 2006
2006 May 08-11 in Munich
Registration is closed.
To get on the waiting-list, please send a short note that explains your existing skills and experience with (a) microarrays, (b) statistics, and (c) computer programming and your motivation for taking this course to t.beissbarth@dkfz.de. Additionally, please tell us your NGFN Förderkennziffer (FKZ), if available.
| Monday, May 08 - First Analysis steps | |||
| 09.00-09.30 | Introduction and overview | Marc Zapatka | |
| 09.30-12.15 | Quality control, normalization and design | Achim Tresch | |
| 13.30-17.00 | Exercises: Introduction to R, cDNA data, affy data | Zapatka Tresch |
|
| Tuesday, May 09 - Exploratory analysis | |||
| 09.00-10.30 | Differential gene expression | Rainer Spang | |
| 10.30-12.00 | Clustering | Jörg Rahnenführer | |
| 12.00-13.00 | Annotation | Marc Zapatka | |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
Rahnenführer Spang Markowetz |
|
| Wednesday, May 10 - 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, May 11 - Pathways | |||
| 09.00-10.00 | Computational Inference of Cellular Networks | Florian Markowetz | |
| 10.15-11.15 | Scoring Gene Ontology terms | Jörg Rahnenführer | |
| 11.30-12.30 | Group testing: global tests, holistic approaches | Ulrich Mansmann | |
| 13.30-17.00 | Exercises: Gene Set Enrichment Analysis, Global Testing and GO-analysis | Ulrich Mansmann Manuela Hummel |
|
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.
This is a course in microarray analysis -- not an introduction to R. Please read the Introduction to R before the course begins.
R sources and package sources can be downloaded from The Comprehensive R Archive Network at http://cran.r-project.org. R-packages you will need if you bring your own laptop are: Biobase, marray, multtest, limma, vsn, arrayMagic, cluster, RColorBrewer, affy, hgu95av2, hgu95av2cdf, lymphoma, estrogen, ALL, annotate, genefilter, multtest, ROC, isis, pamr, e1071, MCRestimate, globaltest, GOstats, hgu133a, Rgraphviz.
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
| Annalisa Ballarini | Universitätsklinikum "Carl Gustav Carus" | Dresden, Germany |
| Holger Laux | LGC | London, UK |
| Alexandra Walijew | Merck | Berlin, Germany |
| Igor Trajkovski | Jozef Stefan Institute | Ljubljana, Slovenia |
| Ivica Slavkov | Jozef Stefan Institute | Ljubljana, Slovenia |
| Bryan O' Sullivan | UCD Conway Institute | Dublin, Ireland |
| Karen Power | UCD Conway Institute | Dublin, Ireland |
| Lukas Heukamp | University Hospital | Bonn, Germany |
| Pedro Lopez-Romero | CNIC Genomics Unit | Madrid, Spain |
| Hana Hartmannová | Center of Inherited Metabolic Diseases | Prague, Czech Republic |
| Lenka Nosková | Center of Inherited Metabolic Diseases | Prague, Czech Republic |
| Ron Ophir | Weizmann Institute | Rehovot, Israel |
| Stefan Bohlander | Klinikum Großhadern | Munich, Germany |
| Hendrik Reuter | Klinikum Großhadern | Munich, Germany |
| Yu-An Dong | MIT | Cambridge (MA), USA |
| Hilde S. Vollan | Epi-Gen, Akershus University Hospital | Akershus, Norway |
| Stefan Scheidl | University Hospital | Innsbruck, Austria |
| Eva Hoster | University Hospital Großhadern | Munich, Germany |
| Pedro Jares | Genomics Unit, IDIBAPS | Barcelona, Spain |
| Oliver Heil | Deutsches Ressourcenzentrum fuer Genomforschung (RZPD) | Heidelberg, Germany |
| Moritz Heinz | Institut fuer med. Biometrie und Epidemiologie | Mainz, Germany |
| Claudia Hartmann | Institut fuer Immunologie, Ludwig-Maximilians-Universiaet | Muenchen, Germany |
Thank you for registering! If you will not be able to attend, please contact t.beissbarth@dkfz.de as soon as possible so that we can notify the people on the waiting list.
How to find us
We meet at the Klinikum Großhadern, Hörsaaltrakt, Floor K O2, Seminarroom 5, Marchioninistraße 15, 81377 München.
Großhadern lies in the south-west of Munich (map).
A detailed how-to-get-there is found here (in german only).
For navigating, you might also find the roadmap and the following directions helpful:
• If you arrive in Munich by plane, take the S-bahn S8 ("Airport line") to Marienplatz.
• If you arrive by train, take any S-bahn or U-bahn to Marienplatz.
• From Marienplatz take U6 to final stop Klinikum Großhadern.
• Leaving the platform, you stand inside a glass pyramid (marked in red in the left figure below).
 |
 |
|
| The red pyramid is the Ubahn-station at which you arrive using U6. The building marked in green is your destination. | This is the inside of the clinical center. The seminarrooms are on the upper right next to the letters "KL". |
Accomodation
You will need to make your own accommodation arrangements. We recommend rooms at the Hotel Neumayr, which lies in Großhadern close to the clinical center. If you want to stay closer to the center of Munich, we recommend hotels in Schwabing, which is 15min by U-bahn from Großhadern. Have a look at Hotel Hauser, Hotel Lettl, or Renner Hotel Savoy.
Further information
Please contact Tim Beißbarth: t.beissbarth@dkfz.de.