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Diffstat (limited to 'loael.tex')
| -rw-r--r-- | loael.tex | 22 |
1 files changed, 10 insertions, 12 deletions
@@ -178,14 +178,12 @@ An important limitation often raised for computational toxicology is the lack of transparency on published models and consequently on the difficulty for the scientific community to reproduce and apply them. To overcome these issues, source code for all programs and libraries and -the databases that have been used to generate this manuscript are made -available under GPL3 licenses. Databases and compiled programs with all +the data that have been used to generate this manuscript are made +available under GPL3 licenses. Data and compiled programs with all dependencies for the reproduction of results in this manuscript are available as a self-contained docker image. All data, tables and figures in this manuscript was generated directly from experimental results -using the \texttt{R} package \texttt{knitR}. A single command repeats -all experiments (possibly with different settings) and updates the -manuscript with the new results. +using the \texttt{R} package \texttt{knitR}. \section{Materials and Methods}\label{materials-and-methods} @@ -523,8 +521,8 @@ variability}\label{intra-database-variability} Both databases contain substances with multiple measurements, which allow the determination of experimental variabilities. For this purpose we have calculated the mean standard deviation of compounds with -multiple measurements, which is roughly a factor of 2 for both -databases. +multiple measurements. Mean standard deviations and thus experimental +variabilities are similar for both databases. The Nestlé database has 567 LOAEL values for 445 unique structures, 93 compounds have multiple measurements with a mean standard deviation @@ -557,11 +555,6 @@ In order to compare the correlation of LOAEL values in both databases and to establish a reference for predicted values, we have investigated compounds, that occur in both databases. -Figure~\ref{fig:comp} shows the experimental LOAEL variability of -compounds occurring in both datasets (i.e.~the \emph{test} dataset) -colored in blue (experimental). This is the baseline reference for the -comparison with predicted values. - Figure~\ref{fig:datacorr} depicts the correlation between LOAEL values from both databases. As both databases contain duplicates medians were used for the correlation plot and statistics. It should be kept in mind @@ -571,6 +564,11 @@ Correlation analysis shows a significant (p-value \textless{} 2.2e-16) correlation between the experimental data in both databases with r\^{}2: 0.52, RMSE: 0.59 +Figure~\ref{fig:comp} shows the experimental LOAEL variability of +compounds occurring in both datasets (i.e.~the \emph{test} dataset) +colored in blue (experimental). This is the baseline reference for the +comparison with predicted values. + \begin{figure} \centering \includegraphics{figures/median-correlation.pdf} |