Courses in Practical DNA Microarray Analysis 2005
2005 September 19-22 in Saarbrücken
| Monday, Sep 19 - First Analysis steps | ||
| 09.00-09.30 | Introduction and overview | Benedikt Brors |
| 09.30-12.15 | Quality control, normalization and design | Tim Beißbarth |
| 14.45-17.00 | Exercises: Introduction to R, cDNA data, affy data | |
| Tuesday, Sep 20 - Exploratory analysis | ||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck |
| 10.30-12.00 | Clustering | Jörg Rahnenführer |
| 12.00-13.00 | Annotation | Benedikt Brors |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
v.Heydebreck Rahnenführer, Markowetz |
| Wednesday, Sep 21 - 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, Sep 22 - 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,
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
| Sachin Kumar | Institute of Medical Microbiology | Giessen, Germany |
| Jyothi Devakumar | . | Bangalore, India |
| Adrian Anghel | Charles Drew University | Los Angeles, USA |
| Richard Gayle | University of South Dakota | USA |
| Elske Franssen | Netherlands Institute for Brain Research | Amsterdam, The Netherlands |
| Frederik de Bree | Netherlands Institute for Brain Research | Amsterdam, The Netherlands |
| Sasithorn Chotewutmontri | Institute for human genetics, University of Mainz | Mainz, Germany |
| Sammy Haege | Institute for human genetics, University of Mainz | Mainz Germany |
| Ivan Borozan | Banting and Best Department of Medical Research | Toronto, CA |
| Prabhakara Choudary | Center for Neuroscience, UC Davies | Davies, USA |
| Sven Wichert | Department for Neurogenetics, MPI for Experimental Medicine | Göttingen, Germany |
| Oliver Bitz | Institut for Molecular Genetics, University of Mainz | Mainz, Germany |
| Jürgen Dönitz | Dept. Bioinformatics, University of Göttingen | Göttingen, Germany |
| Martin Haubrock | Dept. Bioinformatics, University of Göttingen | Göttingen, Germany |
| Jarno Tuimala | CSC, the Finnish IT center for science | Espoo, Finland |
| Volker Jung | Universitätsklinikum des Saarlandes | Homburg, Germany |
| Abdul Karim Sesay | National Institute for Medical Research | London, UK |
| Stefanie Tauber | ARCS: Austrian Research Centers Seibersdorf | Vienna, Austria |
| Francesa Guana | Pharmacogenomic Laboratory, Fondo Edo Tempia | Biella, Italy |
| Andreas Keller | Universitaet des Saarlands | . |
| Ivan Paponov | Universitaet Freiburg, Zentrum fuer Angewandte Biowissenschaften | Freiburg, Germany |
| Lee-Hsueh Hung | Institut für Biochemie, FB08 Justus-Liebig-Universität Gießen | Giessen, Germany |
| Narendra Kaushik | School of Biosciences, University of Cardiff | Cardiff CF10 3US, UK |
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.
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.
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 Florian Markowetz (florian.markowetz@molgen.mpg.de).