Brief Description:
This course provides an introduction to statistical methods for microarray data analysis. Topics to be covered include: model-based analysis of microarray data, design and analysis of microarray experiments, classification in microarray experiments, and clustering of microrray data. This course will have a special emphasis on the methods and algorithms commonly used in microarray data analysis. This course will be served in the form of lectures and (student) presentations.

Time and Place:
Wednesday 10 - 12, TB219
The first lecture: 12.01.2005

Instructors:
Harri Lähdesmäki, M.Sc. and Prof. Olli Yli-Harja
email: harri.lahdesmaki@tut.fi
www: http://www.cs.tut.fi/~harrila
office: TF412

Lectures and exercises:
Lectures and seminar presentations 26 hours, no exercises.

Timetable:

12.01.2005	Lecture 1, slides [pdf]
19.01.2005	Lecture 2, slides [pdf]
26.01.2005	Lecture 3, slides [pdf]
02.02.2005	Lecture 4, slides [pdf]
09.02.2005	Lecture 5, slides [pdf]
16.02.2005	Student presentations Tommi Aho: 3.2 - 3.2.5 (pages 99-108) [pdf] Nikhil: (Dougherty and Brun, 2004) [pdf]
23.02.2005	No lecture
02.03.2005	Exam week
09.03.2005	Student presentations Pekka Ruusuvuori: 3.3 - 3.3.6 (pages 115-123) [pdf] Anwar Haroon: 3.5 - 3.6.2 (pages 127-134) [pdf]
16.03.2005	Student presentations: Jenni Seppälä: 3.2.6 - 3.2.7 (pages 108-114) [pdf]
23.03.2005	Easter holiday
30.03.2005	Student presentations Petri Röytiö: 3.4 - 3.4.7 (pages 123-127) and paper (Braga-Neto and Dougherty, 2004) [pdf] Antti Saarinen: (Dror et al., 2003) [pdf]
06.04.2005	Student presentations Antti Larjo: 4.4 - 4.4.3 (pages 168-175) [pdf]
13.04.2005	Student presentations Jyrki Selinummi: 4.5 - 4.5.4 (pages 175-184) [pdf] Antti Niemistö: 4.6 - 4.9 (pages 185-200) [pdf]
20.04.2005	Student presentations Autio Reija: (Troyanskaya et al., 2002) [pdf]
27.04.2005	Student presentations Carol Rus: 3.7 - 3.9 (pages 134-158) [pdf] Antti Lehmussola: 4.1 - 4.3 (pages 159-168) [pdf]

Requirements:
Participation in the lectures and seminar presentations (a fraction of the total 26 hours), one oral presentation, and the final exam.

Student presentations can be based on the following sections of the course book, or any of the supplementary research articles.

3. Classification in microarray experiments
3.2 - 3.2.5 (pages 99-108) Tommi Aho
3.2.6 - 3.2.7 (pages 108-114) Jenni Seppälä
3.3 - 3.3.6 (pages 115-123) Pekka Ruusuvuori
3.4 - 3.4.7 (pages 123-127) and paper (Braga-Neto and Dougherty, 2004) Petri Röytiö
3.5 - 3.6.2 (pages 127-134) Anwar Haroon
3.7 - 3.9 (pages 134-158) Carol Rus

4. Clustering microarray data
4.1 - 4.3 (pages 159-168) Antti Lehmussola
4.4 - 4.4.3 (pages 168-175) Antti Larjo
4.5 - 4.5.4 (pages 175-184) Jyrki Selinummi
4.6 - 4.9 (pages 185-200) Antti Niemistö

Course material:
Speed, T., Statistical Analysis of Gene Expression Microarray Data, Chapman & Hall/CRC, 2003. [Amazon]

The material will be supplemented by recent research articles. A preliminary list is available here.

Prerequisites:
8001600 Signal Processing for Systems Biology (SPSB) or 809150 Signal Processing Seminar (Signal Processing for Genomics), or otherwise sufficient knowledge in systems biology.

The style of the course will be technical/mathematical, thus basic knowledge of probability, statistics and signal processing is assumed.

Notes:
This course replaces the course 8001600 Signal Processing for Systems Biology during the spring 2005. Lectures will be given either in Finnish or English. The course is accepted as a postgraduate course (but M.Sc. students can participate as well).