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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.

Preliminary Course schedule
 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
von Heydebreck
 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.


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.


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.

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