Microarray Analysis using R and Bioconductor - ICL



Date: Tuesday, June 3, 2014 - Thursday, June 5, 2014
Venue:  Imperial College London, United Kingdom
Registration Opens Date:  4/04/2014
Registration Deadline:  23/05/2014
Participation:  First come, first served


Course overview

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 (Principal Component Analysis, Hierarchical clustering, Scatter plots).

Audience

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.

Syllabus, Tools and Resources

During this course you will learn about:

  • Data standards: Metadata, MIAME 2.0, Isa software suite
  • Data generation: Microarray technology
  • Data analysis: QC & data exploration using R and Bioconductor

Learning Objectives

After this course you should be able to:

  • Identify an R function or operation and describe its use
  • Apply functions and operations to achieve a specific result in R
  • Recognize the importance of Metadata
  • Run and correctly interpret a QC workflow
  • Explore your data using PC, HC, and scatter plots

Course Feedback

Programme

Prerequisites, software and datasets

Install R library script
 

Day 1 - 3rd June 2014 

Day 1 course material

08:30 - 09:00 Registration

09:00 - 09:45 Course introduction and expectations

09:45 - 10:45 General Introduction to R – what is R, console and Rstudio

10:45 - 11:15 Break

11:15 - 12:45 Introduction to R – handling the environment and data types

12:45 - 13:45 Lunch

13:45 - 15:15 Introduction to R – data input/output and basic scripting

15:15 - 15:45 Break

15:45 - 17:30 Plotting – R-packages and the Bioconductor project

18:30     Conference dinner (Restaurant Ognisko)

*

Day 2  - 4th June 2014

Day 2 course material

09:00 - 09:45 Introduction to the diXa project

09:45 - 10:15 Take home lessons day 1

10:15 - 11:15 Overview of microarray/ Affymetrix technology and terminology

11:15 –11:45 Break

11:45 –12:30 Quality Control and preprocessing of Affymetrix arrays introduction

12:30 - 13:30 lunch

13:30 - 14:00 Getting started with metadata

14:00 - 15:00 Quality control and preprocessing of Affymetrix arrays – Hand-on part 1

15:00 - 15:30 Break

15:30 - 17:30 Quality control and preprocessing of Affymetrix arrays – Hand-on part 2

17:30               End of day 2

*

Day 3  - 5th June 2014

Day 3 course material

09:00 - 09:30 Take home lessons day 2

09:30 - 10:15  Data exploration introduction

10:15 - 10:45 Break

10:45 - 12:00 Data exploration – Hands-on part 1

12:00 - 13:00 Lunch

13:00 - 15:00 Data exploration – Hands-on part 2

15:00 - 16:00 Course conclusion

16:00               End of course

*

Registration

Please note that the registration fee of £130 includes:

  • All meals (lunch and refreshment breaks)
  • Course materials
  • Use of a computer in the Imperial College London IT Training Room throughout the course
  • Course dinner on Tuesday 3rd of June

Please note that members of the EMBL-EBI Industry Programme will have their registration fee paid by the Industry Programme. One Nucleus members receive a 40% discount on the registration fee.

*

Trainers & Organisers:

Myrto Kostadima
Rachel Cavill
Florian Caiment
Marcelo Segura
Lars Eijssen

Vera Matser


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