Microarray Analysis using R and Bioconductor - 2014



Date: Tuesday, January 28, 2014 - Thursday, January 30, 2014
Venue:  Maastricht University, Maastricht, Netherlands
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*This course is now closed. If you would like to express an interest in a future similar event please email training@dixa-fp7.eu*

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).

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Programme 

Day 1 - 28th January 2014

download day 1 materials here (zip file 13mb)

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

Conference dinner (venue & time to be confirmed)

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Day 2  - 29th January 2014

download day 2 materials here (zip file 17mb)

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

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Day 3  - 30th January 2014

download day 3 materials here (zip file 6mb)

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

Registration for this course is now closed, only a limited number of places are available on this course. When you want to join, please email the completed registration form to secretariaat-tgx@maastrichtuniversity.nl. Registration closes at 15th December

The registration fee for this course is €110. Payments details are provided in the registration form. Make sure to read them carefully!

Download the registration form here -> registration form

There is an optional 3 course workshop dinner on the 28th January 2014, charged at €25.

Trainers & Organisers:

Laurent Gatto
Rachel Cavill
Florian Caiment
Marcelo Segura
Lars Eijssen

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Dennie Hebels
Lee Larcombe
Sandrien Wansink


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