The course will be held from May 7 - 23, 2007 (both days included)
Lectures and exercises will take place at the Center for
Biological Sequence Analysis at the Technical University of
Denmark, building 208, auditorium 62, in Lyngby.
Monday, May 7
Introduction - Microarray Technology and R Software
- 9.00-9.30
- Introduction to course + pre-test
Hanne Jarmer
- 9.30-10.00
- Break
- 10.00-10.45
- Overview of the microarray technology
(Lecture slides)
- Hanne Jarmer
- 10.45-11.15
- Who are we? - each participant presents briefly
- 11.15-12.00
- Scanning and Image Analysis (Lecture slides)
Hanne Jarmer
- 12.00-13.00
- Lunch Break
- 13.00-13.30
- Introduction to R (Lecture slides) (An Introduction to R)
- Carsten Friis
- 13.30-15.45
- Exercise: Basic R Commands
(Extra exercise)
(Solution,
Extra solution)
- Carsten Friis & Hanne Jarmer
- 15.45-16.00
- Test of the day
- Carsten Friis
Wednesday, May 9
Preprocessing and Introduction to BioConductor
- 9.00-9:30
- Working with R (Lecture slides)
Carsten Friis
- 9:30-10.45
- Exercise: Working with R (Solution)
Carsten Friis & Hanne Jarmer
- 10.45-11:00
- Break
- 11:00-12:00
- Normalization and Expression Index Calculation (Lecture slides)
H. Bjørn Nielsen
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Discussion on microarray data preprocessing
(Questions)
(Solutions)
- H. Bjørn Nielsen & Chris Workman
- 14.00-14.45
- Case story: Application of in vitro gene expression signatures for in vivo cancer response prediction
Dr. Balazs Gyorffy
- 14.45-15.00
- Break
- 15:00-15.45
- Exercise: Applied exercise in preprocessing using BioConductor part I -> homework (Solution)
- Carsten Friis & Hanne Jarmer
- 15.45-16.00
- Test of the day
- Hanne Jarmer
Monday, May 14
Statistical analysis - Experimental Design
- 9.00-9.15
- Applied exercise in preprocessing using BioConductor part II
Carsten Friis
- 9.15-10:00
- Statistical analysis (Lecture slides)
H. Bjørn Nielsen
- 10:00-10:15
- Break
- 10:15-11:15
- Discussion - Statistics
(Questions)
(Solutions)
H. Bjørn Nielsen
- 11:15-12:00
- Experimental Design (Lecture slides)
Hanne Jarmer
- 12.00-13.00
- Lunch Break
- 13.00-15.00
- Introduction to Exercise
- Exercise: Statistical Analysis
- Hanne Jarmer & Carsten Friis
- 15.00-15.15
- Break
- 15:15-15.45
- Case story: Regulatory T cells and Allergy
- Hanne Jarmer
- 15.45-16.00
- Test of the day
- Hanne Jarmer
Wednesday, May 16
Probe Design - Array CGH
- 9:00-9:15
- Homework
- Hanne Jarmer
- 9:15-12:00
- Probe design using OligoWiz 2.0
(Lecture Slides,
Exercise guide,
OligoWiz 2.0 server)
- H. Bjørn Nielsen
- 12.00-13.00
- Lunch Break
- 13.00-15.45
- Array Comparative Genomic Hybridization (aCGH)
(Lecture slides,
Exercise)
- Hanni Willenbrock
- 15.45-16.00
- Test of the day
- Hanni Willenbrock
Monday, May 21
Dimension Reduction and Data Visualization
- 9.00-10:00
- Dimension Reduction: Principal Component Analysis (PCA) and Clustering (Lecture slides)
Chris Workman
- 10:00-10:15
- Break
- 10:15-12:00
- Discussion: Dimension Reduction
(Questions)
(Solutions)
Chris Workman
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Exercise: Dimension Reduction
- Hanni Willenbrock
- 14.00-14:15
- Break
- 14:15-14.30
- Gene Onthology (GO) and KEGG (Lecture slides)
H. Bjørn Nielsen
- 14:30-15:30
- Exercise: GO analysis
(Code). Now for Windows too.
H. Bjørn Nielsen and Hanne Jarmer
- 15.30-15.45
- Test of the day
- H. Bjørn Nielsen
Wednesday, May 23
Integrative Biology
- 9.00-9:15
- Small test - Did you get it?
Hanne Jarmer
- 9.15-10:15
- Integrative Biology (Lecture slides)
Chris Workman
- 10:15-10:30
- Break
- 10:30-11:15
- Biological Networks (Lecture slides)
Chris Workman
- 11:15-12:00
- Discussion: Integrative Biology
(Questions)
(Solutions)
Chris Workman
- 12.00-13.00
- Lunch Break
- 13.00-13.45
- Introduction to CytoScape (Lecture slides)
Carsten Friis
- 13.45-15.30
- Exercise: Integrative Biology (Files)
- Chris Workman
- 15:30-15.45
- Test of the day
Chris Workman
- 15.45-16:00
- Summary of the course - closing remarks
- Hanne Jarmer
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