| Abbrev | Name |
|---|---|
| DP | Denis Puthier |
| JvH | Jacques van Helden |
2016-2017
The instructions for the 2016 personal work can be found here
| Tool | About |
|---|---|
| R | A free software environment for statistical computing and graphics |
| R markdown | Documentation for R markdown language (used for the practicals) |
| Bioconductor | A set of R libraries dedicated to statistical analysis of genomics data. |
| MeV: MultiExperiment Viewer | A Java application designed to allow the analysis of expression data |
| Cluster 3.0 | Implements the most commonly used clustering methods for gene expression |
| java Treeview | Java-based tool to visualize trees prodced by hierarchical clustering togeter with a heatmap with expression proviles. |
| Date | From | To | Subject | Teacher | Concepts | Material |
|---|---|---|---|---|---|---|
| Fri 04/11 | 14:00 | 18:00 | Detecting differentially expressed genes (DEG) with microrarrays | DP | - Hypothesis testing - Student \(t\) statistics - Unbiased estimation of variance - MA plot - Volcano plots -P-value distribution - E-value |
- Basics about Student and Welch’s t test - Detecting differentially expressed genes in microarray data |
| Mon 07/11 | 14:00 | 18:00 | Functional enrichment of DEG | DP | - Functional enrichment statistics - The hypergeometric distribution |
- Theory : on white board - Hypergeometric distribution and enrichment statistics. An example application: DAVID (practical) |
| Tue 08/11 | 14:00 | 18:00 | The multiple ways to correct for multiple testing | JvH | - False positive risk (FPR) - Expected number of false positives (E-value) - Family-Wise Error Rate (FWER) - False Discovery Rate (FDR) |
- Multiple testing corrections (slides) - Multiple testing corrections (practical) |
| Tue 15/11 | 14:00 | 18:00 | Supervised classification | JvH | - Discriminant analysis - Cross-validation (k-fold, LOO) - Data dimensionality and overfitting - Variable selection |
- Introduction to multivariate analysis - Discriminant analysis (slides) - Dimension reduction and PCA - Practical: supervised classification |
| Mon 12/12 | 09:00 | 13:00 | Overview of discrete distributions, with applications to NGS | JvH | - Geometric - Binomial - Poisson -Hypergeometric - Negative binomial |
Tutorial [html][pdf][Rmd] |
| Mon 12/12 | 14:00 | 18:00 | Detecting differentially expressed genes (DEG) with RNA-seq | DP/JvH | - RNA-Seq principles - Normalizing RNA-seq counts -Detecting differentially expressed genes (DEG) |
- RNA-Seq DEG with DESeq2 [html] [pdf] [Rmd] |
| Wed 14/12 | 09:00 | 13:00 | RNA-seq analysis (pursued) | JvH | [] [] |
|
| Wed 14/12 | 14:00 | 18:00 | Preparation of the personal work | DP | Homework: analysis of psoriasis data [html] [Rmd] [bib] |