Homepage
Contributing Bioinformatics Groups
Course Registration
Courses in
Practical Microarray
Data Analysis
Workshops on
Good Statistical
Practice
Course Materials from Past Years
E-Learning Courses in
Practical Microarray
Data Analysis (Beta)
Links to software
and literature
NGFN

Courses in Practical DNA Microarray Analysis 2007

2007 September 24-27 in Dortmund

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, Sep 24 - 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, Sep 25 - 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, Sep 26 - 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, Sep 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

Kalathur Ravikiran ReddyIGBMCFRANCEWaiting List
Miguel Angel PavnnnInst. Recerca. Hosp. STa. Creu i St. PauSpain 
Stefan ThomsenDept of Zoology, University of CambridgeUnited Kingdom 
Mohamed El-SokkaryGSF instituit of soil ecology Neuherberg MunichGermanyCancelled
Francesca Marta Lilja Di LascioDept Statistics, University of BolognaItaly 
Erick TuiranInstitut für Physik, MainzGermany 
Rodrigo LourencoNorth Carolina State UniversityUSA 
GoldenTabs GoldenTabsqkQffhxeUgUSA 
Marek OmelkaCharles University in PragueCzech RepbulicCancelled
GoldenTabs GoldenTabsUwdTlrRYLEYbnNUSA 
Lilian VarricchioIGBMCFrance 
Per LundIGBMCFrance 
Fabio ManzoIGBMCfrance 
Frederik HeinrichDeutsches Rheuma ForschungszentrumDeutschland 
Luiza HandschuhKarol Marcinkowski Medical University Poland 
Irene YujnovskyIGBMCFrance 
Danilo CeschinIGBMCFrance 
Poli CeciliaIGBMCFrance 
markus markusvVdpDLqVKOxVUSA 
Sukhanshi KhandpurSGPGIIndia 
Judi JudiZjiSuKUInzAcVumJjCUSA 
Marco MiceliSeconda Università degli studi di Napoli Italy 
Agnieszka ZmienkoInstitute of Bioorganic Chemistry PASPoland 
Susi Barthblue-drugs GmbHGermany 
Sadegh AzimzadehNIGEBIran 
Sadegh AzimzadehNIGEBIran 
Sonja Vorwerkfebit biotech gmbhGermany 
Divya MehtaGSF ForschuingszentrumGermany 
Tariq MaqboolINSERM Unit 384France 
AHAN DALALUNIVERSITY FO HYDERABADINDIA 
Wieslawa WloszczakInstitute of Bioorganic Chemistry PASPoland 
Mahmoud ElhefnawiDepartment of medical biotechnology, National Research CentreEgypt 
Yinyin YuanWarwick UniversityUK 
Fatemeh AkhoundiShahrekord universityIran 
debtobey debtobeyczstMyFOWKNdokOPxYNFRufKfRY 
debtobey debtobeyCvQlnysljOQQeOtmNMWmLuOXwuH 
debtobey debtobeynEWXRsRKUSCRWfmhchOQcjuePQ 
Mohammad Hassan BaigYeungnam UniversityRepublic of Korea 
Miguel Angel PavonInst. Recerca. Hosp. STa. Creu i St. PauSpainCancelled
Petricele IoanaUniversity of Agricultural Sciences Cluj-NapocaRomania 
Thanh Loan LeAgrucultural Genetics Institute- VietnamVietnamCancelled
olusegun temitope ogbonlayeGroup medical practitionernigeria 
Arif Ratheruniversity of kashmirIndia 
Chae Hwa KwonPusan National University/cancer research insti South Korea 
Jennifer OkoroAbia polyNigeria 
Pouda PanahandehUniversity of BergenNorway 
Merziuziy MerziuziyntcpFyVxCjIPwbdsOUSA 
Samuel ArvidssonUniversity of PotsdamGermanyWaiting List
Arunachalam VadivelCPCRI /ICRISAT, IndiaIndiaWaiting List
Susanna MarquezHospital Clinic / IDIBAPSSpain 
Calin RUSUTechnical University of ClujROMANIA 
Ananta paineHannover Medical SchoolGermanyCancelled
Alireza HaghighiUniversity of OxfordUKWaiting List
kannabiran nandakumardkfzgermanyWaiting List
hanaa zfaculty of agricultureEygptWaiting List
soha AhmedCairo University-faculty of computer scienceegyptWaiting List
Ingrid Liliana Vargas PanessoUniversity of Frankfurt Germany 
Ingrid Liliana Vargas PanessoUniversity of Frankfurt GermanyWaiting List

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, September 24., at 9am. The location and details how to find us will be announced here later.

Accomodation

You will need to make your own accommodation arrangements.

Further information

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

Comments on this webpage