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

DNA Microarray Analysis - #27612

The course will be held from January 7 - 25, 2013 (both days incl.)

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 210, room 162, 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 2013

Monday, January 7

Introduction - Microarray Technology and R Software

9.00-9.30: Introduction to course (Lecture slides)
H. BjÃ¸rn 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); Damian Plichta and Jens Friis-Nielsen
13.30-13.45: Break
13.45-15.30: Exercise: Basic R Commands (Exercise, Extra exercise) (Solution, Extra solution); Damian Plichta and Jens Friis-Nielsen

Tuesday, January 8

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. BjÃ¸rn Nielsen
10.00-10.15: Break
10.15-12.00: Discussion on microarray preprocessing (Questions); H. BjÃ¸rn Nielsen
12.00-13.00: Lunch Break
13.00-14.30: Exercise: Working with R (Lecture slides) (Exercise) (Solution); Jens Friis-Nielsen and Damian Plichta
14.30-14.45: Break
14.45-15.45: Applied exercise in preprocessing using BioConductor (Exercise) (Solution); Jens Friis-Nielsen and Damian Plichta

Wednesday, January 9

Statistical analysis and data visualization

9.00-9.45: Statistical analysis (Section 3.5-3.6) (Lecture slides)
H. BjÃ¸rn Nielsen
9.45-10.00: Coffee Break
10.00-11.15: Exercise: Basic statistical analysis (Exercise, Solution)
Agnieszka S. Juncker and H. BjÃ¸rn 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 Juliet Frederiksen

Thursday, January 10

Advanced statistical analysis and gene annotation

9.00-10.30: Exercise: Advanced statistical analysis (Exercise, Data, Solutions); 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 Juliet Frederiksen
14.45-15.00: Break
15.00-16.00: Exercise: Reading Data into R (Exercise); Damian Plichta and Jens Friis-Nielsen

Friday, January 11

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 Juliet Frederiksen
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 2013); H. BjÃ¸rn Nielsen

Monday, January 14

New generation sequencing

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

Tuesday, January 15

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); Agata Wesolowska
11:00-12:00: Project work (problem formulation); H. BjÃ¸rn Nielsen
12.00-13.00: Lunch Break
13:00-16:00: Project work (problem formulation); H. BjÃ¸rn Nielsen

Wednesday, January 16

Project Work - Problem formulation

10.00-12.00: Project work in (Groups 2013); Office Hours - one or more Teacher(s) can be found in group room 162 (building 210)
15.00: Deadline for problem formulation - hand in max 1/2 page; H. BjÃ¸rn Nielsen

Thursday, January 17

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 162 (building 210)

Friday, January 18 - Thursday, January 24

Project Work