Abbrev  Name 

DP  Denis Puthier 
JvH  Jacques van Helden 
20162017
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  Javabased 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 Pvalue distribution  Evalue 
 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 (Evalue)  FamilyWise 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  Crossvalidation (kfold, 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 RNAseq  DP/JvH   RNASeq principles  Normalizing RNAseq counts Detecting differentially expressed genes (DEG) 
 RNASeq DEG with DESeq2 [html] [pdf] [Rmd] 
Wed 14/12  09:00  13:00  RNAseq analysis (pursued)  JvH  [] [] 

Wed 14/12  14:00  18:00  Preparation of the personal work  DP  Homework: analysis of psoriasis data [html] [Rmd] [bib] 