CBS >> CBS Courses >> DNA Microarray Analysis >> Course Programme

DNA Microarray Analysis - #27612

The course will be held from January 2 - 20, 2012 (both days incl.)

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, room 062, in Lyngby (map).

R can be downloaded and installed locally from cran. Also, an Introduction to R and a reference card to R is available.

Course Programme - January 2012

Monday, January 2

Introduction - Microarray Technology and R Software

9.00-9.30: Introduction to course (Lecture slides)
H. Bjørn Nielsen
9.30-10.15: Overview of the microarray technology (Chapter 1) (Lecture slides); Hanne Jarmer
10.15-11.00: Case story: Gene expression profiling and testicular development; Kirstine Belling
11.00-11.15: Break
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); Francesco Favero
13.30-13.45: Break
13.45-15.30: Exercise: Basic R Commands (Exercise, Extra exercise) (Solution, Extra solution); Francesco Favero, and Marcin Krzystanek

Tuesday, January 3

Preprocessing and Introduction to Bioconductor (R)

9.00-10.00: Normalization and expression index calculation (Section 3.1-3.4) (Lecture slides) (Irizarry et al 2005)
H. Bjørn Nielsen
10.00-10.15: Break
10.15-12.00: Discussion on microarray preprocessing (Questions); H. Bjørn Nielsen
12.00-13.00: Lunch Break
13.00-14.30: Exercise: Working with R (Lecture slides) (Exercise) (Solution); Marcin Krzystanek and Francesco Favero
14.30-14.45: Break
14.45-15.45: Applied exercise in preprocessing using BioConductor (Exercise) (Solution); Marcin Krzystanek and Francesco Favero

Wednesday, January 4

Statistical analysis and data visualization

9.00-9.45: Statistical analysis (Section 3.5-3.6) (Lecture slides)
H. Bjørn Nielsen
9.45-10.00: Coffee Break
10.00-11.15: Exercise: Basic statistical analysis (Exercise)
Agnieszka S. Juncker and H. Bjørn Nielsen
11.15-12.00: Case story: Drug discovery in Alzheimer Disease using microarrays; Simon Rasmussen
12.00-13.00: Lunch Break
13.00-13.45: Dimension reduction: PCA and Clustering (Chapter 4 and 5) (Lecture slides); Agnieszka S. Juncker
13.45-14.00: Break
14.00-15.00: Exercise: Dimension reduction: PCA and Clustering (Exercise); Agnieszka S. Juncker and Kirstine Belling

Thursday, January 5

Advanced statistical analysis and gene annotation

9.00-10.30: Exercise: Advanced statistical analysis (Exercise, Solutions, Data); Hanne Jarmer and Agnieszka S. Juncker
10.30-10.45: Break
10.45-12.00: Exercise: Advanced statistical analysis (continued); Hanne Jarmer and Agnieszka S. Juncker
12.00-13.00: Lunch Break
13.00-14.45: Gene Onthology (GO) and KEGG (Install Cytoscape, Lecture Slides, Exercise ); Simon Rasmussen and Kirstine Belling
14.45-15.00: Break
15.00-16.00: Exercise: Reading Data into R (Exercise); Marcin Krzystanek and Francesco Favero

Friday, January 6

Class prediction and integrative biology

9.00-9.45: Classification (Chapter 8) (Lecture slides); Aron Eklund
9.45-10.00: Break
10.00-11.15: Exercise: Classification Based on DNA Microarray Data (Exercise, Solutions); Aron Eklund and Kirstine Belling
11.15-12.00: Case story: Predicting chemotherapy benefit for breast cancer patients; Aron Eklund
12.00-13.00: Lunch Break
13.00-14.15: Integrative Biology (Exercise); Chris Workman and Agnieszka S. Juncker
14.15-14.30: Break
14.30-15.30: Project introduction (group formation) (Data sets slides, Lecture slides, Groups 2012); H. Bjørn Nielsen

Monday, January 9

New generation sequencing

9.00-9.45: Transcriptomics by Next Generation Sequencing technology (Lecture); Ulrik Plate
9.45-10.00: Break
10.00-11.00: Exercise: Next Generation Sequencing (Exercise); Ulrik Plate and Agnieszka S. Juncker
11:00-12:00: Project work (data set selection and problem identification); H. Bjørn Nielsen
12.00-13.00: Lunch Break
13:00-16:00: Project work (data set selection and problem identification); H. Bjørn Nielsen

Tuesday, January 10

Genome-wide association study analysis

9.00-9.45: Case story: Selecting genetic variation markers for a focused leukemia association study; Agata Wesolowska
9.45-10.00: Break
10.00-11.00: Exercise: Genetic testing for Health, Disease and Ancestry (Exercise); Kasper Nielsen
11:00-12:00: Project work (problem formulation); H. Bjørn Nielsen
12.00-13.00: Lunch Break
13:00-16:00: Project work (problem formulation); H. Bjørn Nielsen

Wednesday, January 11

Project Work - Problem formulation

10.00-12.00: Project work in (groups); Office Hours - one or more Teacher(s) can be found in group room 062 (building 208)
15.00: Deadline for problem formulation - hand in max 1/2 page; H. Bjørn Nielsen

Thursday, January 12

Project Work - Project presentation

9.00-10.00: Problem presentations (10 min pr. group, one slide); Project groups
10.00-12.00: Project work; Office Hours - one or more Teacher(s) can be found in group room 062 (building 208)

Friday, January 13 - Thursday, January 19

Project Work