Courses in Practical DNA Microarray Analysis 2005
2005 Nov 28 - Dec 01 in Berlin
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 florian.markowetz@molgen.mpg.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:
Biobase,
marray,
multtest,
limma,
vsn,
arrayMagic,
cluster,
RColorBrewer,
affy,
hgu95av2,
hgu95av2cdf,
estrogen,
lymphoma,
ALL,
annotate,
genefilter,
multtest,
ROC,
isis,
pamr,
e1071,
MCRestimate,
globaltest,
GOstats,
hgu133a,
Rgraphviz.
| Monday, Nov 28 - 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 | |
| Tuesday, Nov 29 - Exploratory analysis | ||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck |
| 10.30-12.00 | Clustering | Adrian Alexa |
| 12.00-13.00 | Annotation | Marc Zapatka |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
von Heydebreck Markowetz |
| Wednesday, Nov 30 - 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, Dec 01 - Pathways | ||
| 09.00-10.00 | Computational Inference of Cellular Networks | Florian Markowetz |
| 10.15-11.15 | Group testing: global tests, holistic approaches | Ulrich Mansmann |
| 11.30-12.30 | Scoring Gene Ontology terms | Adrian Alexa |
| 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.
R-packages you will need:
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
| Armin Schmitt | Institut für Nutztierwissenschaften, HU Berlin | Berlin, Germany |
| Ralf Jäger | Universitätsklinikum | Marburg, Germany |
| Jose Gadea | Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC | Valencia, Spain |
| Gema Ancillo | Instituto Valenciano de Investigaciones Agrarias (IVIA) | Valencia, Spain |
| Stephan Lehr | Schering AG | Berlin, Germany |
| Martina Messow | IMBEI, Uni Mainz | Mainz, Germany |
| Anja Bauernfeind | Max Delbrück Center for Molecular Medicine | Berlin, Germany |
| Tatjana Luganskaja | Max Delbrück Center for Molecular Medicine | Berlin, Germany |
| Robert Ivanek | Institute of Molecular Genetics | Prague, Czech Republic |
| Petr Divina | Institute of Molecular Genetics | Prague, Czech Republic |
| David Rozado | MPI Molecular Genetics | Berlin, Germany |
| Wasinee Rungsarityotin | MPI Molecular Genetics | Berlin, Germany |
| Jutta Scholven | Institut für Veterinär-Biochemie Freie Universität Berlin | Berlin, Germany |
| Tim M Strom | Institut fuer Humangenetik | Neuherberg/Muenchen, Germany |
| Oliver Stoss | Klinikum Kassel | Kassel, Germany |
| Bernike Kalverda | Netherlands Cancer Institute | Amsterdam, The Netherlands |
| Sven Rahmann | Bielefeld University | Bielefeld, Germany |
| Florian Wagner | RZPD Deutsches Ressourcenzentrum für Genomforschung GmbH | Berlin, Germany |
| Viola Gesellchen | Deutsches Krebsforschungszentrum (DKFZ) | 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 Florian Markowetz as soon as possible so that we can notify the people on the waiting list.
Accomodation
You have to organize accomodation on your own. We recommend rooms at the Harnack-House, Ihnestrasse 16-20, Berlin-Dahlem. From there it's a five minutes walk to the MPI-MG. Please mention the title of the workshop with your registration. Contact information at http://www.harnackhaus-berlin.mpg.de. Also not too far from the institute is Hotel Ravenna in Berlin-Steglitz. Contact: http://www.ravenna-hotel.de.
How to find us
We meet at the Max-Planck-Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin-Dahlem, main building (Turm 2) third floor, big seminar room, on Mon Nov 28 at 9 am. The MPI-MG is next to the underground station Thielplatz (U1). Click here for detailed visitor informations.
Further information
Please contact Florian Markowetz: florian.markowetz@molgen.mpg.de.