diXa: Microarray Analysis using R and Bioconductor
Is this course right for me?
This course is aimed at researchers and scientists (PhD students, post-doc, staff scientist) who will benefit from an introduction to microarray data analysis and training in how to perform simple analysis using R/Bioconductor.
All sessions are a combination of lectures and hands-on. Prerequisites are a life science degree or equivalent experience, basic understanding of microarray techniques, and a basic understanding of biostatistics. No prior knowledge of R or Bioconductor is assumed.
What will I learn?
Participants will receive a basic understanding of the R syntax and ability to manipulate R objects. After this course students should feel comfortable with the R/Bioconductor environment and be in a position to continue their own explorations of the functionality of R and start using R for their basic biostatistics needs. You will understand why Quality Control of microarray is necessary, run a QC workflow and be able to correctly interpret the results. A range of data exploration methods will be reviewed (PCA, Hierarchical clustering, KNN and Kmean, Scatter plots).
| Time | Topic |
|---|---|
| Day 1 - 14th May 2013 - Laurent Gatto | |
| 09:00 - 09:30 | Welcome and registration (Vera Matser) |
| 09:30 - 10:30 | General Introduction to R - what is R, console and Rstudio (Laurent Gatto) |
| 10:30 - 11:00 | Tea/coffee break |
| 11:00 - 12:30 | Introduction to R – handling the environment and data types (Laurent Gatto) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:00 | Introduction to R – data input/output and basic scripting (Laurent Gatto) |
| 15:00 - 15:30 | Tea/coffee break |
| 15:30 - 17:00 | Plotting. R packages and the Bioconductor project (Laurent Gatto) |
| 17:00 | End of day 1 |
| 19:00 | Course dinner at the Red Lion Inn, Hinxton |
| Day 2 - 15th May 2013 - Vera Matser / Dennie Hebels | |
| 09:00 - 09:45 | Introduction to the diXa project (Vera Matser & Stathis Kanterakis) |
| 09:45 - 10:45 | Overview of microarray/Affymetrix technology and terminology (Lars Eijssen) |
| 10:45 - 11:15 | Tea/coffee break |
| 11:15 - 12:00 | Quality control and preprocessing of Affymetrix arrays introduction (Rachel Cavill) |
| 12:00 - 12:30 | Getting started with metadata (Florian caiment) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:00 | Quality control and preprocessing of Affymetrix arrays - Hands on 1 (Rachel Cavill, Florian Caiment & Lars Eijssen) |
| 15:00 - 15:30 | Tea/coffee break |
| 15:30 - 17:00 | Quality control and preprocessing of Affymetrix arrays - Hands on 2 (Rachel Cavill, Florian Caiment & Lars Eijssen) |
| 17:00 | End of day 2 - free evening |
| Day 3 - 16th May 2013 - Marcelo Segura | |
| 09:00 - 09:30 | Data exploration introduction (Marcelo Segura) |
| 09:30 - 10:30 | Data exploration - Hands on 1 (Marcelo Segura) |
| 10:30 - 11:00 | Tea/coffee break |
| 11:00 - 12:50 | Data exploration - Hands on 2 (Marcelo Segura) |
| 12:50 - 13:00 | Concluding remarks (Vera Matser) |
| 13:00 | End of course |
Standard Registration- £150
EMBL-EBI Industry programme members registration - free of charge
Please note that the registration fee includes:
* Lunch and refreshments during the course
* Course materials
* Use of EBI IT Training Room computer during the 2½ day course
* Dinner on Tuesday 14th May
There will be a maximum of 30 participants on this course and registration is on a first come first serve basis. Registration will close on 21st April 2013 at 12:00 (noon) (GMT)
To register for this workshop please use the following link (Items marked * are mandatory. Incomplete registrations will not be processed). You will need to pay by credit card as you submit your registration, therefore please have your card to hand.
This course is now full if you would like to register an interest in a future similar event please do so here>>>>
PLEASE NOTE: Registrants must book their own travel and accommodation.
We would recommend that you book your accommodation at any of the following locations:
Wellcome Trust Conference Centre
Information regarding travelling to the EBI can be found here:
Information regarding further accommodation options can be found here: