diff --git a/knitr/effadj.Rnw b/knitr/effadj.Rnw index bd3134f..cb69826 100755 --- a/knitr/effadj.Rnw +++ b/knitr/effadj.Rnw @@ -482,26 +482,6 @@ The mean of the bootstrap distribution seems consistently larger that the other We see that the large number of dilution steps, as recommended, ensures a low impact of the AE induced standard error on the inference of the $\ddcq$. -% CIC fig -\begin{figure} -\begin{center} -\includegraphics[width=\textwidth]{fig1} -\end{center} -\caption{ - Overview of CIC experiment data. - A: Raw $C_q$-values for different cell lines (samples) for each gene type and sample type. - The point type and colour differentiates the different gene types. - B: Dilution data for - reference genes (\textit{ACTB}, \textit{GAPDH}) and - target genes (\textit{MGST1}, \textit{MMSET}). -} -\label{fig:cqCIC} -\end{figure} - -% CIC table -\input{../output/Table1.tex} - - @@ -524,28 +504,6 @@ The bootstrap method provides a standard deviation similar to the delta method a Regarding the biological interest, we conclude there is evidence for a difference in \textit{miR-127} expression between testicular and nodal DLBCL whilst the data is not compatible with difference in \textit{miR-143} expression. While the AE estimate had no influence in these cases a change in significance is easily imagined in other cases. -% DLBCL fig -\begin{figure} -\begin{center} -\includegraphics[width=\textwidth]{fig2} -\end{center} -\caption{ - Overview of DLBCL testis experiment data. - A: Raw $C_q$-values for different patient samples for each gene type and sample type. - The point type and colour differentiates the different gene types. - B: Dilution data for - reference genes (\textit{RNU-24}, \textit{RNU-6B}) and - target genes (\textit{miR-127}, \textit{miR-143}). -} -\label{fig:cqTestis} -\end{figure} - -% DLBCL table -\input{../output/Table2.tex} - - - - \subsection{Arabidopsis thaliana data} @@ -565,24 +523,6 @@ While this example was selected as a worst-case scenario, it should illustrate t -% Arabidopsis thaliana fig -\begin{figure} -\begin{center} -\includegraphics[width=\textwidth]{fig3} -\end{center} -\caption{ - Overview of \citet{Yuan2008} experiment data. - $C_q$-values against the dilution step for case and control samples. - Dilution data are present for both the target (\textit{MT7}) and reference genes (Tublin, \textit{UBQ}). - The technical duplicates have been averaged out in the analysis. - } -\label{fig:cqYuan} -\end{figure} - -% Arabidopsis thaliana table -\input{../output/Table3.tex} - - \subsection{Simulation study} @@ -613,21 +553,6 @@ Overall, we see that the EC\&VA adjusted estimate is the only procedure consiste Likewise, for many dilutions, the difference between the EC and EC\&VA procedures diminish as the uncertainty of the AE is relatively low. Finally as expected a decrease in FPR corresponds to a decrease in TPR. -% Simulation tab -\input{../output/Table4.tex} - -% Simulation fig -\begin{figure} -\begin{center} -\includegraphics[width=\textwidth]{fig4} -\end{center} -\caption{ - Plot of the false positive rates (FPR, black) and true positive rates (TPR, grey) and their 95 \% confidence intervals achieved simulation experiments for each method at various $p$-value cut-offs (0.05, 0.01, 0.1) shown by solid red horizontal lines. - The FPR and TPR are computed completely analogous to Table~\ref{tab:simexample}. - The rates are plotted for each combination of 4 or 8 samples with 4 or 8 fold dilution curves. -} -\label{fig:simstudy} -\end{figure} \section{Discussion and conclusion} @@ -687,5 +612,86 @@ The Danish Agency for Science, Technology and Innovation, as well as Karen Elise \bibliographystyle{biorefs} \bibliography{references} +\newpage + +% CIC fig +\begin{figure} +\begin{center} +\includegraphics[width=\textwidth]{fig1} +\end{center} +\caption{ + Overview of CIC experiment data. + A: Raw $C_q$-values for different cell lines (samples) for each gene type and sample type. + The point type and colour differentiates the different gene types. + B: Dilution data for + reference genes (\textit{ACTB}, \textit{GAPDH}) and + target genes (\textit{MGST1}, \textit{MMSET}). +} +\label{fig:cqCIC} +\end{figure} + +% CIC table +\input{../output/Table1.tex} + + +% DLBCL fig +\begin{figure} +\begin{center} +\includegraphics[width=\textwidth]{fig2} +\end{center} +\caption{ + Overview of DLBCL testis experiment data. + A: Raw $C_q$-values for different patient samples for each gene type and sample type. + The point type and colour differentiates the different gene types. + B: Dilution data for + reference genes (\textit{RNU-24}, \textit{RNU-6B}) and + target genes (\textit{miR-127}, \textit{miR-143}). +} +\label{fig:cqTestis} +\end{figure} + +% DLBCL table +\input{../output/Table2.tex} + + + +% Arabidopsis thaliana fig +\begin{figure} +\begin{center} +\includegraphics[width=\textwidth]{fig3} +\end{center} +\caption{ + Overview of \citet{Yuan2008} experiment data. + $C_q$-values against the dilution step for case and control samples. + Dilution data are present for both the target (\textit{MT7}) and reference genes (Tublin, \textit{UBQ}). + The technical duplicates have been averaged out in the analysis. + } +\label{fig:cqYuan} +\end{figure} + +% Arabidopsis thaliana table +\input{../output/Table3.tex} + + +% Simulation tab +\input{../output/Table4.tex} + +% Simulation fig +\begin{figure} +\begin{center} +\includegraphics[width=\textwidth]{fig4} +\end{center} +\caption{ + Plot of the false positive rates (FPR, black) and true positive rates (TPR, grey) and their 95 \% confidence intervals achieved simulation experiments for each method at various $p$-value cut-offs (0.05, 0.01, 0.1) shown by solid red horizontal lines. + The FPR and TPR are computed completely analogous to Table~\ref{tab:simexample}. + The rates are plotted for each combination of 4 or 8 samples with 4 or 8 fold dilution curves. +} +\label{fig:simstudy} +\end{figure} + + + + + \end{document}