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 Laurent Modolo committed May 19, 2022 1 2 3 4 5 6 7 8 9 10 --- 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  Laurent Modolo committed Jun 08, 2022 11  slide_level: 2  Laurent Modolo committed May 19, 2022 12  theme: metropolis  Laurent Modolo committed Jun 08, 2022 13  oslides_presentation:  Laurent Modolo committed May 19, 2022 14 15 16 17 18 19 20 21  highlight: tango slidy_presentation: highlight: tango classoption: aspectratio=169 --- # Introduction  Laurent Modolo committed Jun 30, 2022 22 ## Program  Laurent Modolo committed May 19, 2022 23   Laurent Modolo committed Jun 30, 2022 24 25 26 6. Differential expression analysis (Monday 11 July 2022 - 15:30) - Parametric versus non-parametric testing - Differential expression analysis between groups  Laurent Modolo committed May 19, 2022 27  - Regression analysis  Laurent Modolo committed Jun 30, 2022 28  - Multiple testing  Laurent Modolo committed May 19, 2022 29  - Multivariate Differential expression analysis  Laurent Modolo committed Jun 30, 2022 30   Laurent Modolo committed Jul 05, 2022 31 32 33 34 # Hypothesis testing ## Hypothesis testing  Laurent Modolo committed Jul 08, 2022 35 \begin{itemize}  Laurent Modolo committed Jul 05, 2022 36 37  \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  Laurent Modolo committed Jul 08, 2022 38 \end{itemize}  Laurent Modolo committed Jul 05, 2022 39 40 41  ## Hypothesis testing  Laurent Modolo committed Jul 08, 2022 42 \begin{itemize}  Laurent Modolo committed Jul 05, 2022 43 44  \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  Laurent Modolo committed Jul 08, 2022 45 \end{itemize}  Laurent Modolo committed Jul 05, 2022 46   Laurent Modolo committed Jul 08, 2022 47   Laurent Modolo committed Jul 05, 2022 48 \begin{center}  Laurent Modolo committed Jul 08, 2022 49  {\bf We reject $H_0$ with a given risk $\alpha$ and a power $\beta$}  Laurent Modolo committed Jul 05, 2022 50 51 52 53 54 55 56 57 58 59 60 61 62 63 \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}  Laurent Modolo committed Jul 08, 2022 64  \href{https://en.wikipedia.org/}{  Laurent Modolo committed Jul 05, 2022 65 66 67  \includegraphics[width=0.6\textwidth]{img/alpha_beta.png} } \end{center}  Laurent Modolo committed Jun 30, 2022 68 # Parametric versus non-parametric testing  Laurent Modolo committed Jul 05, 2022 69   Laurent Modolo committed Jun 30, 2022 70 # Differential expression analysis between groups  Laurent Modolo committed Jul 05, 2022 71   Laurent Modolo committed Jun 30, 2022 72 ## Differential expression analysis between $2$ groups  Laurent Modolo committed Jul 05, 2022 73   Laurent Modolo committed Jun 30, 2022 74 ## Between $n$ groups  Laurent Modolo committed Jul 05, 2022 75   Laurent Modolo committed Jun 30, 2022 76 # Regression analysis  Laurent Modolo committed Jul 05, 2022 77   Laurent Modolo committed Jun 30, 2022 78 # Multiple testing  Laurent Modolo committed Jul 05, 2022 79 80 81  # Post-selection inference  Laurent Modolo committed Jun 30, 2022 82 # Multivariate Differential expression analysis