diXa: Microarray Analysis using R and Bioconductor

Date:

  Tuesday 14 May 2013

Application opens: 

Thursday 14 February 2013

Application deadline: 

Sunday 21 April 2013

Contact: 

Alison Barker

Registration 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

Red Lion Hinxton

Red Lion Whittlesford

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

Participant Survey