Transcriptomics
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.
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.
| 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 |
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
Course materials can be found at the following link:
/training/sites/ebi.ac.uk.training/files/materials/2008/course_080128_transcriptomics.zip