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---
title: "single-cell RNA-Seq data: Differential expression analysis"
author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
date: "Friday 3 June 2022"
output:
  beamer_presentation:
    df_print: tibble
    fig_caption: no
    highlight: tango
    latex_engine: xelatex
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    slide_level: 2
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    theme: metropolis
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  oslides_presentation:
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    highlight: tango
  slidy_presentation:
    highlight: tango
classoption: aspectratio=169  
---

# Introduction

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## Program
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6. Differential expression analysis (Monday 11 July 2022 - 15:30)
 - Parametric versus non-parametric testing
 - Differential expression analysis between groups
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 - Regression analysis
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 - Multiple testing
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 - Multivariate Differential expression analysis
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# Hypothesis testing

## Hypothesis testing

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\begin{itemize}
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  \item $H_0$: the gene pression is the same between the $2$ groups
  \item $H_1$: the gene pression is not the same between the $2$ groups
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\end{itemize}
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## Hypothesis testing

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\begin{itemize}
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  \item $H_0$: the gene pression is the same between the $2$ groups
  \item $H_1$: the gene pression is not the same between the $2$ groups
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\end{itemize}
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\begin{center}
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  {\bf We reject $H_0$ with a given risk $\alpha$ and a power $\beta$}
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\end{center}

## Hypothesis testing

\begin{itemize}
  \item $\beta$ probability of a Type II error, known as a {\it false negative}
  \item $1 - \beta$ probability of a {\it true positive}, i.e., correctly rejecting the null hypothesis. $1 - \beta$ is also known as the power of the test.
  \item $\alpha$ probability of a Type I error, known as a {\it false positive}
  \item $1 - \alpha$ probability of a {\it true negative}, i.e., correctly not rejecting the null hypothesis
\end{itemize}

## Hypothesis testing

\begin{center}
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  \href{https://en.wikipedia.org/}{
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    \includegraphics[width=0.6\textwidth]{img/alpha_beta.png}
  }
\end{center}
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# Parametric versus non-parametric testing
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# Differential expression analysis between groups
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## Differential expression analysis between $2$ groups
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## Between $n$ groups
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# Regression analysis
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# Multiple testing
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# Post-selection inference

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# Multivariate Differential expression analysis