Microarray Analysis using R and Bioconductor


Date: Tuesday, May 14, 2013 - Thursday, May 16, 2013
Venue:  European Bioinformatics Institute, CB10 1SD, United Kingdom
Registration Opens Date:  Thursday, February 14, 2013
Registration Deadline:  Sunday, April 21, 2013 at 12:00 (GMT)
Participation:  First come, first served

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 analyses 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).

Preliminary Programme
 

Day 1 

09:00 - 09:30 Welcome and registration 
09:30 - 10:30 General Introduction to R – what is R, console and Rstudio
10:30 - 11:00 Break
11:00 - 12:30 Introduction to R – handling the environment and data types
12:30 - 13:30 Lunch - Poster session
13:30 - 15:00 Introduction to R – data input/output and basic scripting
15:00 - 15:30 Break
15:30 - 17:00 Plotting – R-packages and the Bioconductor project
17:00               End of day 1

19:00 Course dinner at the Red Lion Inn, Hinxton

Day 2  

09:00 - 09:45 Introduction to the diXa project 
09:45 - 10:45 Overview of microarray/ Affymetrix technology and terminology
10:45 –11:15 Break
10:15 –12:00 Quality Control and preprocessing of Affymetrix arrays introduction
12:00 –12:30 Getting started with metadata
12:30 - 13:30 lunch
13:30 - 15:00 Quality control and preprocessing of Affymetrix arrays – Hand-on part 1
15:00 - 15:30 Break
15:30 - 17:00 Quality control and preprocessing of Affymetrix arrays – Hand-on part 2
17:00               End of day 2 - free evening

Day 3  

09:00 - 09:30 Data exploration introduction
09:30 - 10:30 Data exploration – Hands-on part 1
10:30 - 11:00 Break
11:00 - 12:50 Data exploration – Hands-on part 2
12:50 - 13:00 Closing remarks
13:00               End of course

Registration

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 35 participants on this course and registration is on a first come first serve basis. 

Registration for this event is now closed because the maximum number of participants has been reached. If you would like to express an interest in a future similar event please email training@dixa-fp7.eu

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 and further accomodation options can be found here:

Trainers & Organisers:

Laurent Gatto
Stathis Kanterakis
Rachel Cavill
Florian Caiment
Lars Eijssen
Marcelo Segura

Dennie Hebels
Vera Matser

For more information or questions email training@dixa-fp7.eu