Advanced Microarray Data Analysis: Class Discovery and Class Prediction

NorFA course

Course Programme 2004

17. - 21. May 2004


Lo-skolen, Elsinore

Closed for application

The course is free for all participants, however, a fixed price will be charged for lodging, meals and an excursion (ca. 5000 dkr. in shared room. An additional 1200 dkr. will be charged for single room). Ph.d. students in the Nordic countries may apply to the NorFa Bioinformatics Network program for partial financial support (see application form) to cover part of course expenses (10-15 grants will be available with an average 4000 dkr. for each student; exact amount depending on travel costs)

Aim and Content
The course will focus on statistical analysis methods that can be applied to data consisting of gene expression values obtained by microarray technology, as well as their applications. These methods include feature selection, class discovery and classification. A few new hot subjects within microarray data analysis will also be introduced.
Initial data treatment (e.g. image analysis, normalization and expression index) will not be explored in the course.

The courses are open to all qualified applicants. Research students (PhD students) and young post-doctoral researchers (post-docs) from the Nordic countries.

Academic Prerequisites
Participants should have prior knowledge of DNA microarray technology and basic microarray analysis techniques.
Required prerequisites should correspond to: A Biologist's Guide to Analysis of DNA Microarray Data Knudsen, S., Wiley, New York (2002).
For the exercises, the participants should be familiar with the R statistical package. An introduction to R may be read cursorily in advance.

Travel information
Elsinore (In danish: Helsingør) is located approximately 50 km north from Copenhagen.
If you arrive with plane: The closest airport is Copenhagen airport. Directly from the airport you can go with the train to Elsinore (approx. 1 hour 10 min). The train leaves every 20 min. You can buy a train ticket at the airport. From Elsinore station there is 2-3 km to the course center (LO-skolen). You can take a local bus, however it can be recommended to take a taxi from there to LO-skolen. Helsingør Taxa: Phone +45 49 22 35 35.
Public transport in Denmark: You can make plans for public transport in Denmark on Rejseplanen

Accommodation details
Course duration: Monday 10 am - Friday 5 pm (at latest).
The course price covers accommodation and meals from Monday (including a light breakfast at 9.30, check-in at noon) until Friday afternoon (incl. afternoon coffee/cake, check-out 9.00 a.m.).
If you arrive earlier or leave later, please make your own bookings at the LO-skolen (or another hotel nearby, see Elsinore turist office).
When making additional bookings at LO-skolen, please inform them, that you, on your own, are making extra room booking for before or after course only, and specify for them if you are staying in a single or double room during the course together with the reservation number 138222.

Participants are required to bring their own laptops (Operative system: Windows 2000/XP).
However, we do have a few labtops available in case you are not able to bring your own (please let us know in advance if this is the case, at latest May 10th)
Make sure that you have the administration rights to the computer that you bring with you, so you can install new software/packages during the course.

Required software
(to install prior to the course)
R (version 1.9.0): The setup program (rw1090.exe) can be downloaded here.
More information about R-installlation on Windows can be found in the R Installation and Administration Manual or R for Windows FAQ.
Additional packages can be installed from the RGui. So far you may install the pamr, multtest, e1071, sma, ipred, cluster, rpart, randomForest,limma, marrayClasses, marrayInput, marrayNorm, marrayPlots, supclust and affy packages. However, more packages might have to be installed during the course.
For the clustering exercise a java toolbox, Macheon, will be needed. The executable program can be downloaded from here, and further information about Macheon can be found in the Software Manual. In order to run Macheon on your computer you need to have java installed. You can find a download site for java on the Sun homepage, however you can also download version J2SE 1.4.2 directly from here.

Course material
Course material will be distributed at the beginning of the course.

At the beginning of the course a short presentation of all participants will be arranged. Each participant will get around 2 min for the presentation. You are welcome to bring 1 overhead with you for the presentation.

Course credit
At the end of the course all participants will receive a course diploma. The credit for the course (in ECTS Point) will be specified later.

Course Coordinators
Jeppe Skytte Spicker
Hanni Willenbrock
Agnieszka S. Juncker
Steen Knudsen

Centre for Biological Sequence Analysis
Technical University of Denmark
Building 208
DK-2800 Lyngby

The course is sponsered by NorFA