Verified Commit 1a3b2177 authored by Laurent Modolo's avatar Laurent Modolo
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5_pseudo_time: update

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......@@ -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
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......@@ -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
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