MDA11
Massive Data Analysis (using Babelomics)Course Timetable |
MDA11 | Massive Data Analysis (using Babelomics) |
Mon, Feb 21st |
Day #1
|
09:30 - 11:00 |
Introduction Why microarrays? Pre- and post-genomics hypothesis testing: a note of caution. Design of experiments. Data preprocessing and normalization. Unsupervised analysis (clustering). Supervised analysis (gene selection, predictors). Functional annotation. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 |
Normalization (theory) Getting rid of unwanted variability from sources other than the experimental conditions assayed. Methods for Affymetrix and two-colour microarrays. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Normalization (practical session) Normalization of Affymetrix and two-colour arrays |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
Gene selection (theory) Methods for selecting differentially expressed genes among two or more experimental conditions, correlated to a continuous variable or correlated to survival. How to deal with the multiple-testing problem. Gene selection (practical session) Practical exercises with different methods and different types of gene selection problems. |
Tue, Feb 22nd |
Day #2
|
09:30 - 11:00 |
Predictors (theory) Gene selection in the context of class prediction. How to deal with the selection bias problem. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 |
Predictors (practical session) Building class predictors with different methods. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Clustering (theory) An overview of different clustering methods: hierarchical clustering, SOM, SOTA and k-means |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
Clustering (practical session) Practical exercises with different clustering methods: hierarchical clustering, SOM, SOTA and k-means |
Wed, Feb 23rd |
Day #3
|
09:30 - 11:00 |
Functional interpretation of microarray experiments (theory) Understanding the biological roles played by the genes in the experiments. Using different types of information for the functional annotation of microarray experiments: gene ontology, InterPro motifs, transcription factor binding sites, gene expression in other experiments, etc. The babelomics suite. How to deal (again) with the multiple testing problem. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 |
Functional interpretation of microarray experiments The Babelomics suite. Different methods and criteria for the functional interpretation of microarray experiments. FatiGO and FatiScan from the Babelomics suite. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Practical exercises covering all the aspects taught |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Correction of the exercises and get together. |
Course Homepage |
Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: Jan 20th 201\ |