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BioSys: DNA Microarray Analysis
6 day course, May 2007
With high throughput methods such as DNA microarrays, DNA content or gene expression may be measured in both prokaryotes and eukaryotes.
Microarray data is together with DNA sequence data the most abundant biological data source and fundamental to understanding the dynamics of biological systems.
This course will highlight the biological questions that may be answered by microarray analyses including expression analysis, DNA copy number studies (array CGH) and ChIP-chip assays.
The participant will be introduced to the statistical programming language R, and learn to perform interesting microarray analyses on their own.
When and where
The course will take place Mondays and Wednesdays from May 7th to 23rd (6 days)
at DTU in Lyngby, building 208 room 062.
The course days starts at 9:00 and end 16:00
Course Program
Content
The technology behind GeneChips and cDNA arrays; normalization of data;
statistical significance of changes in gene expression; experimental design;
reduction and visualization of large data matrices: PCA and clustering;
functional analysis (GO) and case stories. R programming: reading data in/out,
manipulate data, write simple scripts, follow and modify cookbook instructions,
and perform statistical analysis. Homework: R programming and exercises.
Scope and form
Lectures, discussions, computer exercises and programming exercises (homework)
Aim/objectives
The aim of this course is to give the students a profound knowledge of methods for microarray analysis as well as the ability to apply computerized analyses on gene expression data.
Learning objectives
After the course the student should be able to:
- Account for the individual steps in a general microarray analysis
- Explain the overall theoretical principles behind the individual steps in the analysis
- Account for the preconditions and assumptions in the individual steps of the analysis
- Independently apply a basic microarray analysis
- Manipulate simple data structures, use and adapt cookbook R code, and write own functions in the program package R
Prerequisite
- Some understanding of molecular biology
- Basic statistics
- No pre-knowledge of R is required
Course Language:
English
Computer requirements
Some Windows PC's are available from DTU, but homework must be done on your own PC. For the maximal benefit of the course we recommend you bring your own computer.
Use your own portable computer for exercises (updated. 4th of January 2006)
Teachers
Carsten Friis, Hanne Jarmer, Chris Workman, Hanni Willenbrock and H. Bjørn Nielsen
from the Systems Biology of Gene Expression group at CBS
Textbook
Guide to Analysis of DNA Microarray Data, 2nd Edition
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