Courses in Practical DNA Microarray Analysis 2008
2008 March 3-6 in Heidelberg
The course is open for registration.
Application: 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. You may use the Registration Form.
If you bring your own laptop, be sure to have installed the following packages:
affy, Biobase, marray, multtest, limma, vsn, arrayMagic, cluster, RColorBrewer, hgu95av2, hgu95av2cdf, estrogen,
ALL, annotate, genefilter, multtest, ROC, isis, pamr, e1071, MCRestimate, GlobalAncova, globaltest, GOstats,
hgu133a, Rgraphviz.
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, Mar 3 - First Analysis steps | |||
| 09.00-09.30 | Introduction and overview | Benedikt Brors | |
| 09.30-12.30 | Quality control, normalization and design | Tim Beissbarth | |
| 14.00-17.00 | Exercises: Introduction to R, cDNA data, affy data | Beissbarth, Brors | |
| Tuesday, Mar 4 - Exploratory analysis | |||
| 09.00-10.30 | Differential gene expression | Holger Fröhlich | |
| 10.30-12.00 | Clustering | Tim Beissbarth | |
| 12.00-13.00 | Annotation | Marc Zapatka | |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
Zapatka, Beissbarth, Fröhlich | |
| Wednesday, Mar 5 - Molecular Diagnosis | |||
| 09.00-10.30 | Molecular Diagnosis and Model Selection | Holger Fröhlich | |
| 10:045-12.15 | Classification with PAM and Random Forest | Markus Ruschhaupt | |
| 13.30-17.00 | Exercises: Molecular Diagnosis | Ruschhaupt, Fröhlich | |
| Thursday, Mar 6 - Pathways | |||
| 09.00-10.00 | Computational Inference of Cellular Networks | Achim Tresch | |
| 10.15-11.15 | Group testing: global tests, holistic approaches | Manuela Hummel | |
| 11.30-12.30 | Scoring Gene Ontology terms | Manuela Hummel | |
| 13.30-17.00 | Exercises: topGO, global testing, gene set enrichment analysis | Hummel, Alexa, Ruschhaupt | |
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
| Johannes Klein | TU Braunschweig, Institut of Microbiology | Germany | |
| Boyke Bunk | TU Braunschweig, Institute for Microbiology | Germany | |
| Tobias Koschubs | Gene Center, AG Cramer, University of Munich | Germany | |
| Frederic Quignon | Univ Metz | France | |
| Piotr Gawron | Poznan University of Technology | Poland | |
| Ramona Schmid | Boehringer Ingelheim/ DKFZ Theoretical Bioinf | Germany | |
| Athanasios Zovoilis | Institute of Human Genetics, Univ of Göttingen | Germany | |
| Setia Pramana | Censtat Hasselt University | Belgium | Cancelled |
| Arthur Gitome | University Hasselt Belgium | Belgium | Cancelled |
| Lana Fernandes | CReSA | Spain | |
| Anna Tomas | UAB | Spain | |
| Martin Sill | DKFZ | Germany | |
| Kannabiran Nandakumar | DKFZ | Germany | |
| Ina Talke | Bioquant / HIP, Universität Heidelberg | Germany | |
| Arturo Sanz Sanz | Erasmus MC | The Netherlands | |
| Maria Dinkelacker | DKFZ | Germany | |
| Constantin Kuehl | Innere Medizin III, Universität Heidelberg | Deutschland | |
| Jinyong Hu | Max planck instiute for plant breeding | Germany | Cancelled |
| Jana Rolff | MDC Berlin | Germany | |
| Reza Sohrabi | Virginia Tech | USA | |
| Cornelia Spycher | Institute of Parasitology, University of Zürich, | Switzerland | |
| Laura Morf | Institute of Parasitology, Zürich, Switzerland | Switzerland | |
| Sandra Andorf | FBN, Dummerstorf | Germany | |
| Heiko Mannsperger | DKFZ Heidelberg | Germany | |
| Michael Becker | Max-Delbrueck-Center for Molecular Medicine | Germany | |
| Simge Aykan | Radboud University | The Netherlands | Cancelled |
| Thomas Wolf | DKFZ | Germany | |
| Yvonne Koch | DKFZ | Germany | |
| Tobias Meissner | Universiaetsklinikum Heidelberg | Germany | |
| Thierry Reme | IRB-INSERM U847 | France | Cancelled |
| Jerome Moreaux | CHU Montpellier | france | |
| Bernard Klein | INSERM | France | |
| Dirk Hose | Universitätskliniukm Heidelberg | Germany | |
| Anja Seckinger | Dept. of Internal Med., Heidelberg University | Germany | Cancelled |
| Guerkan Bal | Charite Universitätsmedizin | Deutschland | |
| Carsten Sticht | ZMF Uniklinik Mannheim | Germany |
Thank you for registering! If you will not be able to attend, please contact Tim Beißbarth as soon as possible so that we can notify the people on the waiting list.
How to find us
We meet Monday, March 3., at 9am at the IPMB building, in the computer room in the 3rd floor. The IPMB lies on the science campus of the university of Heidelberg, "Im Neuenheimer Feld", building 364 (see map).
The closest airport (by time, not by distance) is Frankfurt/Main. It is approximately 90km away, but has a nice high-speed train connection to Heidelberg via Mannheim. Travel by train is about 1 hour. Other airports would be Karlsruhe/Baden Airport and Stuttgart. Travel directions are at the DKFZ web site, too.
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.
- see map
Further information
Please contact Tim Beissbarth: t.beissbarth@dkfz.de.