University of Copenhagen


Statistical analysis of gene expression data with R and Bioconductor
August 17 - 21, 2009

With follow-up workshop August 24 and 25:
Gene expression based on sequencing technologies

Time and Place

The course takes place from Monday, August 17 to Friday, August 21, 2009.

The lectures and exercises will take place at the

University of Copenhagen
Copenhagen Biocenter
Ole Maaløes Vej 5
DK-2200 Copenhagen Ø
Room(s) 4-0-24 (4-0-5)
The course is organized with a mix of lectures and supervised computer exercise sessions each day.

Course Description

The course aims to give Ph.D.-students in statistics as well as other Ph.D.-students a good introduction to data analysis of gene expression experiments using R and Bioconductor. The primary lectures/teachers of this course are international researchers on gene expression data analysis and/or developers of R-packages.
The course will be taught by the following: The list of topics that will be covered looks as follows:

All participants will receive a certificate of participation.

ECTS-credits: 5


We will use R 2.9.1 and have provided an installation guide to ease the installation.

The participants are expected to have prior experience with R and statistics in general, and an interest in the biological questions. To be more specific, you are required to know how to use R for standard statistical analyzes such as doing a t-test or a linear regression, and you should know about the fundamental data structures such as vectors, lists and data frames. The participants are also expected to bring their own laptop for the exercises. We require that all participants prior to the course install the latest version of R and the latest version of Bioconductor (which releases will be announced on this web page when settled). The precise details for the required installation of R and the installation of required additional packages will be provided.



All days are 9.00-17.00, but it is possible that we will end a little earlier some of the days. Lunch is 12.30 - 13.30. Every day will include combinations of lectures and computer labs. Both lectures and exercises take place in room 4-0-24 (we also have room 4-0-5 available).
  • Monday 17/8. Introduction to gene expression data and the biological questions, data formats and representations in R, R applications and R programming (Margaret Taub, Kasper Daniel Hansen, Niels Richard Hansen)

    Introduction to gene expression:
    - technologies, data formats, the data representation in Bioconductor, preprocessing and normalization, quality assessment

    Introduction to R and Bioconductor

    Simple differential expression example

  • Tuesday 18/8. Affymetrix microarray analysis and visualization (Laurent Gautier).

    Processing expression data from microarrays
    - Manufacturing technologies: photolithography, micromirrors, inkjet-like, pin-spotted
    - Probe selection
    - Background correction (includes norm+exp model of RMA)
    - Normalization (includes quantiles normalization used in RMA)
    - Probeset summary (include medianpolish used in RMA)

    Graphics for microarray data
    - heatmaps, genomic contexts, network contexts, inspection of what comes out of tests

  • Wednesday 19/8. Linear models and Limma (Mark Robinson).

    Introduction to Limma and background correction

    Moderated t-tests and simple linear models

    Linear modeling, more advanced experimental designs and moderated F-tests

    Gene set tests


  • Thursday 20/8. Integrative genomics (Vincent Carey).
  • Friday 21/8. Analysis of data from sequencing based expression technologies (Margaret Taub, Kasper Daniel Hansen).

Registration and Payment

Registration has closed for now. There are more than 65 registered participants and with a total limit of 50 participants it has been decided to close the registration.

The number of participants is limited to a total of 50, and the places are given after a first come first serve principle according to the following quota:
Danish Ph.D.-students 20
Other Ph.D.-students/academia 15
Others 15

The registration fee is:

Ph.D.-students and other academia: DKK 1000,-
Non-academia*: DKK 4000,-

which, among other things, will cover lunch, coffee/tea and the hand-out material.

*Employees in BioSys member companies can register at the academia rate of DKK 1000, cf. the BioSys member list. However, the total number of these BioSys discounts is limited to 15 and allocated on a first come first serve basis.

The deadline for payment is

July 1, 2009

The details for payment via bank transfer (only possibility) are as follows:

Payment to:

Department of Mathematical Sciences
University of Copenhagen
Universitetsparken 5
DK-2100 Copenhagen Ø

For Danish bank transfers:

Account number: 3001 4115212125

For international bank transfer:

IBAN-code: DK41 3000 4115212125
Bank Address: Danske Bank A/S, Holmens Kanal 2, 1090 København K, Denmark

IMPORTANT; the following reference and information must be included for all transfers:

Bioconductor 2009
Your name

It is VERY IMPORTANT that you provide the number given above. If the space is limited you should ONLY provide the reference number 501000 as a minimal reference. Do NOT try to write other parts of the full reference number, if you can not write the full number.

Remember also that for INTERNATIONAL bank transfers you must pay ALL the additional costs.



Handout material

All participants will receive hand-out material covering the lectures and the computer labs. For additional reading we recommend the books:

Bioinformatics and Computational Biology Solutions
Using R and Bioconductor

Bioconductor Case Studies

Directions and accommodation

Please find information on directions and accommodation on our website. Note that we have no possibility to give financial support for participants.


University of Copenhagen


Niels Richard Hansen
Department of Mathematical Sciences