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Courses in Practical DNA Microarray Analysis 2007

2007 May 07-10 in Regensburg

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, May 7 - 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, May 8 - 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, May 8 - 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, May 10 - 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

Narendra KaushikSchool of Biosciences, University of CardiffUnited Kingdom 
Kathrin JuerchottRZPD - Dt. Ressourcenzentrum fuer GenomforschungGermany 
Susanne HaiderUniversität WienÖsterreich 
Anke Thielfebit biotech gmbHGermany 
Caroline ReiffRowett Research InstituteUK 
Laura GianninoIstituto Sperimentale Italiano Lazzaro SpallanzaItaly 
Justine RochonZentrum für Klinische Studien (ZKS) RegensburgGermany 
Matthias GondanUniversity of RegensburgGermanyCancelled
Marijana RadonjicTNOThe Netherlands 
Andre ScheragInstitute of Med. Biometry and EpidemiologyGermany 
Andre BoorsmaUniversity of MaastrichtNetherlands 
Alexander ReußKKS MarburgGermanyCancelled
Christian BaranyiUni. Vienna Austria 
Adrian SchroederUniversity of TuebingenGermany 
Ruben AlcazarMax Planck Institut für ZüchstungforschungKoeln 
Marta BitrianMax Planck Institute for plant breeding researchGermany 
Liping XuUni TuebingenGermany 
Nga LaoDept. of Genetics, Trinity CollegeIreland 
Dejan LazarevicSISSA/ISASItaly 
Helena KrmacSISSA/ISASItaly 
Nicolas VillacortaMax Planck Institute for Plant Breeding ResearchGermany 
Benoukraf TouatiCIML INSERM-CNRSMarseille 
Ondrej ValinaUniversity of Southern DenmarkDenmark 
Xue DongCUBIC center University CologneGermany 
Andreas DraegerUniversity of TuebingenGermanyCancelled
Friederike TrognitzARC Seibersdorf research centersAustria 
Farzana AbubakarThe Aga Khan UniversityPakistan 
Kalathur Ravi Kiran ReddyIGBMCFranceWaiting List
Samuel ArvidssonPotsdam UniversityGermanyWaiting List
Won Kyong ChoBotanisches Institut in MünchenGermanyWaiting List
Dr. G. Madhavi SastryW/o Dr. G. Narahari Sastry, AvH fellow, MunichgermanyWaiting List
Andrea SoltysovaFac. of sciences UK, dep.of molecular biologySlovakiaWaiting List
Susi Barthblue-drugs GmbHGermanyWaiting List
Yasmina BauerActelionCHWaiting List
Kathrin MichelMax Planck Institut für neurologische ForschungGermanyWaiting List
YALÇIN TAHTALIMAKRO FARMA istanbul/TURKİYEWaiting List
Michael RehliUniversity of RegensburgGermanyWaiting List
Carol El ChartouniUniversity of RegensburgGermany 
Elmar SchillingUniversity of RegensburgGermany 
Andreas MaurerUni Klinikum Regensburg Germany 

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, May 07., at 9am at the University Clinic, building A2 seminar room 1, in Regensburg (see map). The clinic can be reached by car from the A3 exit "Regensburg Klinikum" or by public transport from the Regensburg central station using bus line 6 to the final destination "Klinikum" in about 10 minutes. The bus station "Bustreff Albertstrasse" is in viewing distance of the central station around the corner at the "Galgenbergbridge".

Accomodation

You will need to make your own accommodation arrangements. We recommend rooms at the Hotel Apollo, which is a five minutes walk away from the clinical center. You could also look for a hotel in the center of Regensburg, which is aproximately 10 minutes by bus. See map.

Further information

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

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