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Courses in Practical DNA Microarray Analysis 2007

2007 November 26-29 in Munich

The course is open for registration.

Application: 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. You may use the Registration Form.

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.

Preliminary Course schedule
 Monday, Nov 26 - First Analysis steps
09.00-09.30 Introduction and overview Benedikt Brors
09.30-12.30 Quality control, normalization and design Tim Beissbarth
14.00-17.00 Exercises: Introduction to R, cDNA data, affy data Beissbarth, Brors
 Tuesday, Nov 27 - Exploratory analysis
09.00-10.30 Differential gene expression Anja von Heydebreck
10.30-12.00 Clustering Jörg Rahnenfüührer
12.00-13.00 Annotation Benedikt Brors
14.00-17.00 Exercises: Differential gene expression
Clustering
Rahnenführer, Heydebreck
 Wednesday, Nov 28 - Molecular Diagnosis
09.00-10.30 Molecular Diagnosis Rainer Spang
10.30-11.30 Classification with PAM and Random Forest Markus Ruschhaupt
11.30-12.30 Model Assessment and Selection Rainer Spang
13.30-17.00 Exercises: Molecular Diagnosis Ruschhaupt, Spang
 Thursday, Nov 29 - Pathways
09.00-10.00 Computational Inference of Cellular Networks Achim Tresch
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
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

Miguel Angel Pavon RibasInst. Recerca. Hosp. STa. Creu i St. PauSpain 
Liudmila LiutskoUniversity of Barcelona, phD studentSpainCancelled
Simon GeimerBotanisches Institut in MünchenGermany 
Samuel ArvidssonUniversity of PotsdamGermany 
Ana TomasicInstitut Rudjer BoskovicCroatia 
Yannick Le PriolIMTSSAFrance 
Sofia MosciUniversita degli studi di GenovaItaly 
Vered Chalifa-CaspiBen-Gurion University of the NegevIsraelCancelled
Raffaella CalligarisSISSA/ISAS (Internat. School for Advan. Studies)Italy 
Wieslawa WloszczakInstitute of Bioorganic Chemistry PASPolandCancelled
Subramanian Arun KumarUniversity of ReadingUnited Kingdom.Cancelled
Tan Mei LanUniversiti Sains MalaysiaMalaysia 
Ester FeldmesserWeizmann Institute of ScienceIsrael 
Ahmet R. OzturkBilkent University / TurkeyTurkey 
AKINSOLA LAWALYABA COLLEGE TECHNOLOGYNIGERIA 
Peter KoningsGhent University HospitalBelgium 
Kirstin MeyerBayer Schering PharmaGermany 
Arunprababhu DhanapalENEARoma, Italy 
Divya MehtaGSF ForschuingszentrumGermany 
Nannan YangFaculty of Medicine, Univ. of Tromso, NorwayNorwayCancelled
Peter NovotaUniversity of GoettingenGermanyCancelled
mohamed adel elsokkaryfaculty of pharmacy,Mansoura University egypt 
Aadath AadathAadathGermany 
Mohsen HajheidariMax-planck Institute for plant breeding researchGermany 
Kutay Karatepebilkent universityturkeyCancelled
Emma CadmanRoyal Veterinary CollegeUnited Kingdom 
Michal StrehovskyFaculty of Informatics, Masaryk UniversityCzech republic 
mohamed mohamed elsokkaryGSF NeuherbergGermany 
nicolas boulangertagc ERM 206FRANCE 
Xia DongTUMGermany 
Damaris MatokeKenya Medical Research InstituteKenyaWaiting List
Pieter van BokhovenFree University AmsterdamThe Netherlands 
Grit HutterKlinikum Grosshadern, Med III, KKG LeukemieGermany 
Zlatana PasalicGSF-KKG LeukemiaGermany 
KAZEEM OLABODE LEMBOYENIGERIAN EXPORT IMPORT BANKLAGOS NIGERIAWaiting List
Md. Asad Ud-DaulaGSF-Institute of Ecological chemistryD-85764 Neuherberg, Germany 
GILBERT OSAYEMWENREUNIVERSITY OF BENIN NIGERIAnigeriaWaiting List
Sarrah Ben MWageningen universityThe Netherlands 
Katharina HeimGSF ForschungszentrumGermany 
necati cakirUniversity of Trakya, Department of RheumatologyTurkey 
Kivanc ErgenKocaeli University, Biophysics DepartmentTurkeyWaiting List
Sukhdeep SinghAmbala College of Engineering & Applied ResearchIndiaWaiting List
Sukhdeep SinghAmbala College of Engineering & Applied ResearchIndiaWaiting List
Ananta paineHannover Medical SchoolGermanyWaiting List
Alireza HaghighiUniversity of OxfordUKWaiting List
ANANTH RAJANCENTRE FOR MARINE SCIENCE AND TECHNOLOGYINDIAWaiting List
MARY VICTABHARTHIAR UNIVERSITYINDIAWaiting List
Sebastian WaszakGene Centre MunichGermanyWaiting List
Benjamin WasmerMax-Planck-Institute for Ornithology Germany 
Rafal WoycickiWarsaw Agricultural UniversityPoland 
Matilda UlmiusPure and Applied Biochemistry, Lund UniversitySwedenWaiting List
Aly SomaaPAMCHSDahrhan 31932. POBox 946Waiting List
Kristel Van SteenGhent University HospitalBelgium 

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 at the Klinikum Großhadern, Hörsaaltrakt, Floor K O2, Seminarroom 5, Marchioninistraße 15, 81377 München.
Großhadern lies in the south-west of Munich (map). A detailed how-to-get-there is found here (in german only). For navigating, you might also find the roadmap and the following directions helpful:
• If you arrive in Munich by plane, take the S-bahn S8 ("Airport line") to Marienplatz.
• If you arrive by train, take any S-bahn or U-bahn to Marienplatz.
• From Marienplatz take U6 to final stop Klinikum Großhadern.
• Leaving the platform, you stand inside a glass pyramid (marked in red in the left figure below).

The red pyramid is the Ubahn-station at which you arrive using U6. The building marked in green is your destination.   This is the inside of the clinical center. The seminarrooms are on the upper right next to the letters "KL".

Accomodation

You will need to make your own accommodation arrangements. We recommend rooms at the Hotel Neumayr, which lies in Großhadern close to the clinical center. If you want to stay closer to the center of Munich, we recommend hotels in Schwabing, which is 15min by U-bahn from Großhadern. Have a look at Hotel Hauser, Hotel Lettl, or Renner Hotel Savoy.

Further information

Please contact Tim Beissbarth: t.beissbarth@dkfz.de.

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