Courses in Practical DNA Microarray Analysis 2006
2006 September 25-28 in Saarbrücken
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.
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.
| Monday, Sep 25 - First Analysis steps | ||
| 09.00-09.30 | Introduction and overview | Marc Zapatka |
| 09.30-12.15 | Quality control, normalization and design | Tim Beissbarth |
| 13.30-17.00 | Exercises: Introduction to R, cDNA data, affy data | Beissbarth, Zapatka |
| Tuesday, Sep 26 - Exploratory analysis | ||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck |
| 10.30-12.00 | Clustering | Jörg Rahnenführer |
| 12.00-13.00 | Annotation | Marc Zapatka |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
Alexa, Rahnenführer |
| Wednesday, Sep 27 - Molecular Diagnosis | ||
| 09.00-10.30 | Molecular Diagnosis | Rainer Spang |
| 10.30-11.30 | Classification with PAM and Random Forest | Markus Ruschhaupt |
| 11.30-12.30 | Model Assessment and Selection | Rainer Spang |
| 13.30-17.00 | Exercises: Molecular Diagnosis | Ruschhaupt, Rahnenführer |
| Thursday, Sep 28 - 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 | Adrian Alexa |
| 13.30-17.00 | Exercises: Gene Set Enrichment Analysis, Global Testing and GO-analysis | Hummel, Alexa, Tresch |
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.
R-packages you will need:
Biobase,
marray,
multtest,
limma,
vsn,
arrayMagic,
cluster,
RColorBrewer,
affy,
hgu95av2,
hgu95av2cdf,
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
| An De Bondt | Johnson & Johnson Pharmaceutical RD | Beerse, Belgium | |
| Renate Effner | IBE Muenchen | Munic, Germany | |
| Wouter Eijgelaar | University of Maastricht Department of Pathology | Maastricht, Netherlands | |
| Kristine Kleivi | Medical Biotechnology, VTT | Turku, Finland | |
| Andras Treszl | SE 1st Department of Pediatrics | Budapest, Hungary | |
| Duan Jun | Southwest University of China | Chongqing, China | |
| Lukas Chavez | Max-Planck-Institut for Molecular Genetics | Berlin, Germany | |
| Jan Wuyts | Flanders Interuniversity Inst. for Biotechnology | Gent, Belgium | |
| Daniela Marconi | University of Bologna | Bologna, Italy | |
| Catelijne Stortelers | Netherlands Cancer Institute | Netherlands | |
| Santosh Anand | TIGEM (Telethon Institute of Genetics&Medicine) | Napoli, Italy | |
| Ana Rotter | national institute of biology | Ljubljana, Slovenia | |
| Alan Magee | Trinity College | Dublin, Ireland | |
| Petra Kralj | University on Ljubljana | Ljubljana, Slovenia | |
| Stefan Bonn | Max-Planck Institute for Medical Research | Heidelberg, Germany | |
| Holger Fröhlich | DKFZ | Heidelberg, Germany | |
| Alexander Polizos | Bioacademy | Athens, Greece | |
| Qihua Tan | Odense University Hospital | Odense, Denmark | |
| Li Jiang | Danish Institute of Agricultural Sciences | Tjele, Denmark | |
| Mari Peltola | University of Turku | Turku, Finland | |
| Henri Sara | University of Turku | Turku, Finland | |
| Natalia Kan | BASF | Ludwigshafen, Germany | |
| Konstantin Khodosevich | Klin. Neurobiologie, Univ. Klinik | Heidelberg, Germany |
Thank you for registering! This course is fully booked and closed for registration. 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 at the Max-Planck-Institut für Informatik, Building 46.1, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany. Detailed visitor information are found here. Map here.
Accomodation
You have to organize accomodation on your own. We recommend rooms at
• Hotel Seewald in Saarbruecken-Dudweiler. Good and friendly budget-priced hotel close to the university campus and to the Max Planck Institute, in 10-15 minutes walking distance, bus connections also available.
• Domicil Leidinger in Saarbruecken. More upscale hotel close to the city center.
Further information
Please contact the local organizer Jörg Rahnenführer (rahnenfj@mpi-sb.mpg.de) or Tim Beißbarth (t.beissbarth@dkfz.de).