diff --git a/5_pseudo_time/img/monocle_1.png b/5_pseudo_time/img/monocle_1.png new file mode 100644 index 0000000000000000000000000000000000000000..0f59633b9080bdd8c29bb2b4c9e90cb5eb00a619 Binary files /dev/null and b/5_pseudo_time/img/monocle_1.png differ diff --git a/5_pseudo_time/img/pseudo_time.png b/5_pseudo_time/img/pseudo_time.png new file mode 100644 index 0000000000000000000000000000000000000000..1f2830175b1718ed5d7957682c6745c2cb52e753 Binary files /dev/null and b/5_pseudo_time/img/pseudo_time.png differ diff --git a/5_pseudo_time/pseudo_time.Rmd b/5_pseudo_time/pseudo_time.Rmd index b701331a3153245ae8105ac055bd3d608cad6f26..800760288bd2ea663ff8993c16bbc7b919deabd8 100644 --- a/5_pseudo_time/pseudo_time.Rmd +++ b/5_pseudo_time/pseudo_time.Rmd @@ -43,8 +43,30 @@ classoption: aspectratio=169 # Continuous clustering + +\begin{columns} +\column{0.5\textwidth} +one RNA-Seq experiment constitutes a {\bf time series}, with each {\bf cell representing a distinct time point} along a continuum. + +\column{0.5\textwidth} +one RNA-Seq experiment constitutes a {\bf time series}, with each {\bf cell representing a distinct time point} along a continuum. +\begin{center} + \href{http://www.nature.com/doifinder/10.1038/nbt.2859}{ + \includegraphics[with=0.8\textwidth]{img/pseudo_time.png} + } +\end{center} +\end{columns} + # Path detection +## Monocle 1 + +\begin{center} + \href{http://www.nature.com/doifinder/10.1038/nbt.2859}{ + \includegraphics[with=0.8\textwidth]{img/monocle_1.png} + } +\end{center} + # Cycle detection # Velocity diff --git a/6_dea/dea.Rmd b/6_dea/dea.Rmd index a2ccb32ebbc126e96b927fca68a8d4a7b0513f49..1a6131e3a33f59b992ee87bbdb3104aa09a45cf8 100644 --- a/6_dea/dea.Rmd +++ b/6_dea/dea.Rmd @@ -42,6 +42,43 @@ classoption: aspectratio=169 - Multivariate Differential expression analysis 6. Differential expression analysis (Monday 11 July 2022 - 15:30) +# Hypothesis testing + +## Hypothesis testing + +\begin{itemize*} + \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 +\end{itemize*} + +## Hypothesis testing + +\begin{itemize*} + \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 +\end{itemize*} + +\begin{center} + \bf We reject $H_0$ with a given risk $\alpha$ and a power $\beta$ +\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} + \href{https://en.wikipedia.org/wiki/Power_of_a_test#/media/File:Statistical_test,_significance_level,_power.png}{ + \includegraphics[width=0.6\textwidth]{img/alpha_beta.png} + } +\end{center} + # Parametric versus non-parametric testing # Differential expression analysis between groups ## Differential expression analysis between $2$ groups diff --git a/6_dea/dea.pdf b/6_dea/dea.pdf deleted file mode 100644 index 0a8b6b9ff4431389700e2e885f6779ee0aa8656f..0000000000000000000000000000000000000000 Binary files a/6_dea/dea.pdf and /dev/null differ diff --git a/6_dea/img/alpha_beta.png b/6_dea/img/alpha_beta.png new file mode 100644 index 0000000000000000000000000000000000000000..7eec2a980b55e6ed01f4abae7c55b5f8b233f57c Binary files /dev/null and b/6_dea/img/alpha_beta.png differ