spacer
spacer
EBITrainingEBI User Training ProgrammeHands-onTranscriptomics

Hands-on training at EBI - Transcriptomics

Course Summary
Course DetailsTitle: Transcriptomics
Date: 28-30 January 2008
Venue: Hinxton, Cambridge, UK
Organisers: Gabriella Rustici, Vicky Schneider
Admin Support: Alison Barker and Janet Copeland
Registration Deadline: 6th January 2008

About this Course

This course provides an introduction to Transcriptomics incorporating and using the related EBI resources and practicals, trainer-guided demonstration of when, why and how to use them. You will learn about different microarray applications, Designing a microarray experiment, microarray data analysis and links to other EBI resources for microarray gene set analysis.
Top

Topics include

  • Microarray technology: how is the field evolving?
  • High throughput sequencing techniques
  • digital expression
  • ArrayExpress
  • Experimental design; statistics behind microarray; Hypothesis testing; Array quality metrics; Normalisation; Introduction to limma
  • Overview of the principles and methods for differentially expressed genes identification: t-test; ANOVA; False Discovery Rate; more on limma, Expression Profiler and Bioconductor
  • Looking for biological patterns in the data: Clustering; Principal Component Analysis (PCA); Meta analysis; Gene set analysis- Expression Profiler and Bioconductor, GO and Reactome.
Top

Course requirements

Participants should have a minimum degree in a biological discipline, including laboratory and clinical staff as well as specialists in related fields. Preference will be given to those actively engaged or soon to commence microarray research/analysis.

The training is free, however we need to charge participants an administration fee of £25 per day.

Registration closed

Trainers


trans.gif
Roman Laskowski
Gabriella
Rustici
trans.gif		 trans.gif
Misha Kapushesky
Misha
Kapushesky
trans.gif		 trans.gif
Asad Rahman
David
Croft
trans.gif		trans.gif
Asad Rahman
Rachael
Huntley
trans.gif


Top

Guest Speakers

  • Nuno L. Barbosa-Morais
  • Matt Ritchie
Top

Program Contents

The course content is now available to download for people who attend the course.

Time Topic Trainer/Speaker
Day 1 Misha Kapushesky and Gabriella Rustici
13:00 – 13:30 Registration  
13:30 - 15:00 Microarray technology: how is the field evolving? Misha Kapushesky
15:00 - 15:15 Coffee
15:15 - 16:00 Microarray Data Storage: ArrayExpress Gabriella Rustici
16:00 – 17:00 Hands on: ArrayExpress  
Day 2 Matt Richie and Nuno Barbosa-Morais
9:00 - 10:30 Lecture (quality assessment, pre-processing and experimental design)  
10:30 - 11:00 Coffee
11:00 - 12:30 Hands on: limma (pre-processing practical)  
12:30 - 13:30 Lunch
13:30 - 15:00 Lecture (assessing differential expression using linear models)  
15:00 - 15:30 Coffee
15:30 - 17:00 Hands on: limma (continue with pre-processing practical. Start differential expression practical)  
Day 3 Matt Richie, Nuno Barbosa-Morais, Gabriella Rustici, Rachael Huntley, Reactome
9:00 - 10:30 Lecture (clustering, classification)  
10:30 - 11:00 Coffee
11:00 - 12:30 Hands on: limma (complete differential expression practical)  
12:30 - 13:30 Lunch
13:30 - 15:00 Expression Profiler, lecture/practical Gabriella Rustici
15:00 - 15:15 Coffee
15:15 - 17:00 Link to other EBI resources for gene set analysis: Go & REACTOME Rachael Huntley and David Croft

Download course description as pdf


Top






spacer
spacer