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

GTPB Homepage

IGC Homepage

Last updated:   Jan 20th 201\