Courses in Practical DNA Microarray Analysis 2006
2006 November 27-30 in Heidelberg
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 t.beissbarth@dkfz.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:
affy, Biobase, marray, multtest, limma, vsn, arrayMagic, cluster, RColorBrewer, hgu95av2, hgu95av2cdf, estrogen,
ALL, annotate, genefilter, multtest, ROC, isis, pamr, e1071, MCRestimate, GlobalAncova, globaltest, GOstats,
hgu133a, Rgraphviz.
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, Nov 27 - First Analysis steps | |||
| 09.00-09.30 | Introduction and overview | Marc Zapatka | |
| 09.30-11.00 | Quality control, normalization and design | Tim Beissbarth | |
| 11.15-12.45 | Analysis of Tiling-Array Data | Wolfgang Huber | |
| 14.00-17.00 | Exercises: Introduction to R, cDNA data, affy data | Beissbarth, Zapatka, Huber | |
| Tuesday, Nov 28 - Exploratory analysistd> | |||
| 09.00-10.30 | Differential gene expression | Anja von Heydebreck | |
| 10.30-12.00 | Clustering | Jörg Rahnenfüührer | |
| 12.00-13.00 | Annotation | Marc Zapatka | |
| 14.00-17.00 | Exercises: Differential gene expression Clustering |
Rahnenführer, Kaderali, Zapatka | |
| Wednesday, Nov 29 - Molecular Diagnosis | |||
| 09.00-10.30 | Molecular Diagnosis and Model Selection | Holger Fröhlich | |
| 10:045-12.15 | Classification with PAM and Random Forest | Markus Ruschhaupt | |
| 13.30-17.00 | Exercises: Molecular Diagnosis | Ruschhaupt, Fröhlich | |
| Thursday, Nov 30 - Pathways | |||
| 09.00-10.00 | Computational Inference of Cellular Networks | Achim Tresch | |
| 10.15-11.15 | Group testing: global tests, holistic approaches | Manuela Hummel | |
| 11.30-12.30 | Scoring Gene Ontology terms | Adrian Alexa | |
| 13.30-17.00 | Exercises: Global testing,Gene-Set-Enrichment, GO | Mansmann, Hummel, Alexa | |
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.
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
| Ben Nota | Vrije Universiteit Amsterdam | Netherlands | |
| Stephanie Boelz | Verfuegungslabor der Kinderklinik | Germany | |
| Oscar Harari | Universidad de Granada | España | Cancelled |
| Dan Lin | Universiteit Hasselt | Belgium | |
| Riccarda Rischatsch | Biozentrum | Basel | Waiting List |
| Ma. Florencia Lucca | INTA | Argentina | |
| Hamid Zarrini | Waiting List | ||
| Violeta Madzharova | Student, Ruprecht-Karls-University of Heidelberg | Germany | |
| Haluk Yuzugullu | bilkent university | ankara/turkey | |
| Coral del Val | DKFZ-Granada University | Spain | |
| Alessandra Chesi | SISSA/ISAS Trieste | Italy | Cancelled |
| Segun Adeyemi Fatumo | |||
| Stefano Gustincich | SISSA | Italy | Cancelled |
| Rocio Celeste Romero Zaliz | Dept. Computer Science and A.I. (DECSAI) | Spain | |
| Deirdre Corcoran | |||
| Kiran Mandapati | The Centre for Genomic Application | INDIA | Waiting List |
| Suzy Van Sanden | Universiteit Hasselt | Belgium | |
| Ammad Khan | Shaukat Khanum Memorial Cancer Hospital | Pakistan | |
| Naira Naouar | Waiting List | ||
| Tobias Bauer | DKFZ | Germany | |
| Marion Hirt | IMGM Laboratories | Germany | |
| Lennart Opitz | Uni Goettingen, Transkriptomanalyselabor | Germany | |
| zur granevitze | Hebrew University Jerusalem Israel | Israel | |
| Steven Van Laere | University Antwerp | Belgium | |
| ILse Van der Auwera | University Antwerp | Belgium | |
| Mali Salmon | Bar Ilan University, Ramat Gan, Israel | Israel | |
| Hakan Baykus | Rikilt | The Netherlands | |
| Cristina Rubio Escudero | University of Granada | Spain | |
| Özlem Gögebakan | DIfE | Germany | |
| Regine Brandt | Fakultaet fuer klinische Medizin | Germany | |
| Abdul Sesay | MRC NIMR | England | |
| Valeria Lima Passos | Maastricht University | The Netherlands | Cancelled |
| Radek Blatny | Cancelled | ||
| Sridevi Balaraman | Cologne University Bioinformatics Center | Germany | |
| Maria Papatriantafyllou | DKFZ | Germany | |
| Victoria Dominguez-Bohler | INSTITUT PASTEUR | France | |
| Vincent Negre | INSERM | France | Waiting List |
| Yvonne Edwards | University College London | England |
Thank you for registering! If you will not be able to attend, please contact Tim Beißbarth as soon as possible so that we can notify the people on the waiting list.
How to find us
We meet Monday, November 27., at 9am in the German Cancer Research Center (DKFZ) main building, room H824 (8. floor). The DKFZ lies on the science campus of the university of Heidelberg, "Im Neuenheimer Feld", building 280.
This document may be helpful in finding the Neuenheimer Feld in Heidelberg: anfahrt_dkfz.pdf. Unfortunately it is in German only, but contains a number of very detailed maps guiding you to the DKFZ (INF 280).
The lectures take place in different locations on the different days, the practical work will be carried out in the computer room of the IPMB (INF 364, 3rd floor). See course locations
Accomodation
You will need to make your own accommodation arrangements.
• The most useful website for this is the Heidelberg tourist information: http://www.cvb-heidelberg.de.
• The IBIS hotel is a generic budget hotel, close to the train station, and in walking distance from the course venue and from downtown: http://www.ibishotel.com.
• The hotel Frisch is right next to the university campus: http://www.cafe-frisch.de.
Further information
Please contact Tim Beissbarth: t.beissbarth@dkfz.de.