Courses in Practical DNA Microarray Analysis 2004
June 14 - 17 in Berlin
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, June 14 | ||
| 09.00-10.30 | First analysis steps | Wolfgang Huber |
| 11.00-12.30 | Differential gene expression | Anja von Heydebreck |
| 13.30-14.30 | First steps in R | Florian Markowetz |
| 14.45-17.00 | Exercises: Exploring cDNA data | Wolfgang Huber |
| Tuesday, June 15 | ||
| 09.00-10.30 | Exploratory data analysis | Jörg Rahnenführer |
| 10.30-11.30 | Resampling and the bootstrap | Axel Benner |
| 11.30-12.00 | Screening by ROC curve analysis | Axel Benner |
| 13.30-14.30 | Quality Control | Wolfgang Huber |
| 14.45-17.00 | Exercises: 2x2 factorial design | Wolfgang Huber |
| Wednesday, June 16 | ||
| 09.00-10.30 | Molecular Diagnosis | Rainer Spang |
| 10.30-11.30 | Classification by Support Vector Machines | Florian Markowetz |
| 11.30-12.30 | Model Assessment and Selection | Axel Benner |
| 13.30-17.00 | Exercises: classification, model selection | Florian Markowetz Axel Benner |
| Thursday, June 17 | ||
| 09.00-11.00 | Annotation | Benedikt Brors |
| 11.00-12.30 | Design of microarray experiments | Ulrich Mansmann |
| 13.30-17.00 | Exercises: Experimental Design | Ulrich Mansmann |
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 June 14 at 9 am. The MPI-MG is next to the underground station Thielplatz (U1). Click here for detailed visitor informations.
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 in Berlin or Heidelberg.
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.
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], a 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. Basics are explained in Introduction to R.
Participants
| • | Ana Conesa | Center of Citrus Genomics Instituto Valenciano de Investigaciones Agrarias, Moncada (Valencia), Spain. | |
| • | Andrew Harrison | Biochemistry and Molecular Biology Dept. University College London, UK. | |
| • | Caroline Johnston | Biochemistry and Molecular Biology Dept. University College London, UK. | |
| • | Ilhem Diboun | Biochemistry and Molecular Biology Dept. University College London, UK. | |
| • | Surendra Bansal | V. P. Chest Institute, University of Delhi, India. | |
| • | Susanne Schwenke | Schering AG, Berlin, Germany. | |
| • | Hannes-Friedrich Ulbrich | Schering AG, Berlin, Germany. | |
| • | Sascha Thewes | Robert Koch-Institut, Berlin, Germany. | |
| • | Katherina Zakikhany | Robert Koch-Institut, Berlin, Germany. | |
| • | Maximiliano Corredor-Adámez | Institute of Biology, Leiden University, The Netherlands. | |
| • | Andre Mäurer | MPI IB, Berlin, Germany. | |
| • | Yu Wang | GSF - National Research Center for Environment and Health, Neuherberg, Germany. | |
| • | Achim Tresch | Fraunhofer Institut SCAI, Sankt Augustin, Germany. | |
| • | Thomas Schlitt | EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. | |
| • | Letizia Magnoni | Sienabiotech, Siena, Italy. | |
| • | Tracey J Lamb | National Institute for Medical Research, London, UK. | |
| • | Marina Pollán | Cancer Epidemiology Unit, National Center for Epidemiology, Madrid, Spain. | |
| • | Gunther Höning | Clinical center, University of Mainz, 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
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.
Further information
Please contact Florian Markowetz: florian.markowetz@molgen.mpg.de.