Time and Place
The course takes place from Monday, August 17 to Friday, August 21,
The lectures and exercises will take place at the
University of Copenhagen
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.
| 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:
- Laurent Gautier, DTU, Denmark
- Mark Robinson, WEHI Bioinformatics, Australia
- Vincent Carey, Harvard Medical School, USA
- Margaret Taub, UC Berkeley, USA
- Kasper Daniel Hansen, UC Berkeley, USA
- Niels Richard Hansen, University of Copenhagen, Denmark
All participants will receive a certificate of participation.
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
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:
Department of Mathematical Sciences
University of Copenhagen
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,
IMPORTANT; the following reference and information must be
included for all transfers:
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.
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 Case Studies
Please find information on directions and accommodation on our website. Note that we have no possibility to give financial support for