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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


O Monday, January 7

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)
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


O 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. 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)
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

O Wednesday, January 9

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, Solution)
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 Juliet Frederiksen

O 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

O 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. Bjørn Nielsen

O 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. Bjørn Nielsen
12.00-13.00
Lunch Break
13:00-16:00
Project work (data set selection and problem identification)
H. Bjørn Nielsen

O 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. Bjørn Nielsen
12.00-13.00
Lunch Break
13:00-16:00
Project work (problem formulation)
H. Bjørn Nielsen

O 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. Bjørn Nielsen

O 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)

O Friday, January 18 - Thursday, January 24

Project Work

10.00-12.00
Office Hours - one or more Teacher(s) can be found in group room 162 (building 210r)

O Thursday, January 24

Poster Printing

14.00 Deadline for paying Agnieszka S. Juncker Dkr 250 for poster printing and sending poster files (pdf) to Agnieszka S. Juncker
Poster Requirements
O Friday, January 25

Poster Session - In the hall in front of CBS (building 208, top floor)

10.00-12.00
Poster Session part I (exam)
12.00-13.00
Lunch Break
13.00-15.00
Poster Session part II (exam)

O Wednesday, January 23 - Thursday, January 24
Course evaluation on CampusNet
Please, use your student number and password to login

Some additional cookbooks
Singular Value Decomposition (SVD)
Gene Set Enrichment Analysis
Annotational Analysis (web-based)
KEGG annotation analysis (R based)
How to annotate using biomaRt
About R packages and how to install them