diXa: Microarray Analysis using R and Bioconductor
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Date:
Tuesday 14 May 2013Application opens:
Thursday 14 February 2013Application deadline:
Sunday 21 April 2013Contact:
Alison BarkerRegistration closed
Overview
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).
Additional information
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:
Programme
| 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 |
