5_pseudo_time: update

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

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