Microarray & high throughput sequencing data analysis with Bioconductor
Is it right for me?
- This course consists of lectures and hands-on labs. Days 1 to 4 will focus on all aspects of the data analysis of microarray experiments including preprocessing, quality assessment, differential expression, machine learning, etc. Additional talks will address genotyping and image analysis applications. Day 5 will cover the analysis of high throughput sequencing (HTS) data, focusing on RNA-seq and ChIP-seq as well as the crucial aspects of HTS data management.
- Participants are expected to have some familiarity and experience with programming languages, preferably R, as well as with genomic data handling. A basic understanding of the statistical and computational issues associated with microarray and HTS data analysis will be beneficial.
What will it cover?
- Normalization and pre-processing.
- Differential expression.
- Probe design and annotation.
- Genotyping, Phenotyping and Image Analysis.
- Quality assessment, Data Management.
- Presentation and Hands On Learning.
Speakers
- Wolfgang Huber (EMBL Heidelberg)
- Nuno Barbosa Morais (Cambridge University)
- Bernd Fischer (EMBL Heidelberg)
- Richard Pearson (University of Manchester)
- Gregoire Pau (EMBL Heidelberg)
- Simon Anders (EMBL Heidelberg)
- Audrey Kauffmann (Bordeaux University)
| Time | Topic |
|---|---|
| Day 1 - Sunday 31 January 2010 | |
| Arrival and Dinner at The Arundel House Hotel, Chesterton Road, Cambridge | |
|
Day 2 - Monday 01 February 2010 Download a zip folder of the day's materials here: Monday.zip |
|
| 09:00 - 10:30 | Normalization and pre-processing (Wolfgang Huber) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Differential expression: moderated t, filtering, multiple testing (Wolfgang Huber) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Hands-on |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Hands on |
|
Day 3 - Tuesday 2 February 2010 Download a zip folder of the day's materials here: Tuesday.zip |
|
| 09:00 - 10:30 | Differential expression: Linear models (Nuno Barbosa-Morais) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Probe deisgn + annotation (Nuno Barbosa-Morais) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Hands On |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Hands On |
|
Day 3 - Wednesday 3 February 2010 Download a zip folder of the day's materials here: Wednesday.zip |
|
| 09:00 - 10:30 | Machine Learning (Bernd Fischer) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 12:45 | Genome-wide association studies of copy number variants (Richard Pearson) |
| 12:45 - 13:15 | Lunch |
| 13:15 - 14:00 | R workbench demo (Andrew Tikhonov) |
| 14:00 - 15:30 | Practicals |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Practicals |
|
Day 4 - Thursday 4 February 2010 Download a zip folder of the day's materials here: Thursday.zip |
|
| 09:00 - 10:30 | Quality Assessment (Audrey Kauffmann, Gabriella Rustici) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Image Analysis and Cellular Phenotyping (Gregoire Pau) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Practicals |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Practicals |
|
Day 5 - Friday 5 February 2010 Download a zip folder of the day's materials here: Friday.zip |
|
| 09:00 - 10:30 | HTS: RNA-seq, ChIP-seq, quality assessment, data management (Simon Anders/Anglea Goncalves/Nicholas Luscombe) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | ...contd |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Practicals |
| 15:30 - 16:00 | Tea Break |
| 16:00 - close | Practicals, close and survey |
Registration for this course will open on 3 November 2009. Registration will be via a selection process therefore applicants should be aware that, in order to be considered for a place on this course, they MUST submit a letter of motivation (max 50 words) explaining their reasons for attending this course, together with a short CV. Information on how to submit this additional information is contained in your completed application for registration. The selection process will take place w/c 14 December.Successful applicants will be notified by 18 December 2009.
Please complete the registration form in full, making note of your ID and password. Items marked * are mandatory. Incomplete registrations will not be processed. Note: Online payment will be requested by credit card should your application be successful. Please do not begin the registration process unless you can pay the full fee as no bursaries are available.
Cost:
Registration Fee = £650.00
Please note that the registration fee includes all food and accommodation for 5 nights in shared rooms, in the 3* Arundel Hotel, Cambridge.
Registration Closed.
The course materials are available online using the following links: