Courses in Practical DNA Microarray Analysis 2006
2006 Feb 27 - Mar 02 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.
| Monday, Feb 27 - First Analysis steps | ||
| 09.00-09.30 | Introduction and overview | Benedikt Brors |
| 09.30-12.15 | Quality control, normalization and design | Tim Beissbarth |
| 13.30-17.00 | Exercises: Introduction to R, cDNA data, affy data | |
| Tuesday, Feb 28 - Exploratory analysis | ||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck |
| 10.30-12.00 | Clustering | Adrian Alexa |
| 12.00-13.00 | Annotation | Benedikt Brors |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
von Heydebreck Markowetz |
| Wednesday, Mar 01 - 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, Mar 02 - 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.
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
| Viktor Stranecky | Institute of Inherited Metabolic Disorders | Prague, Czech Republic |
| Alena Cizkova | Institute of Inherited Metabolic Disorders | Prague, Czech Republic |
| Amir M.Saeed | Karolinska Institute | Stockholm, Sweden |
| Wolfram Langer | Schering | Berlin, Germany |
| Robert Wagner | RZPD | Berlin, Germany |
| Lin Gan | IZKF Biomat | Aachen, Germany |
| Vasso Theodorou | Netherlands Cancer Institute | Amsterdam, The Netherlands |
| Sebastian Bauer | Charite | Berlin, Germany |
| Willem Talloen | Biometrics and Clinical Informatics | Beerse, Belgium |
| Katarina Cankar | National Institute of Biology | Ljubljana, Slovenia |
| Alex Lam | Roslin Institute | Midlothian, Scotland UK |
| Franz-Josef Müller | Zentrum für Integrative Psychiatrie | Kiel, Germany |
| Sonia Shah | Bloomsbury Centre for Bioinformatics | London, UK |
| Tobias Schulze | Max Delbrück Center | Berlin, Germany |
| Heike Pospisil | Center for Bioinformatics | Hamburg, Germany |
| Marc Weimer | DKFZ Central Unit Biostatistics | Heidelberg, Germany |
| Epameinondas Fritzilas | CEBITEC | Bielefeld, Germany |
| Benjamin Otto | Universitätsklinikum | Hamburg, 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 Feb 27 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.