Visually guided preprocessing of bioanalytical laboratory data using an interactive R notebook (pguIMP)

Abstract

Abstract The evaluation of pharmacological data using machine learning requires high data quality. Therefore, data preprocessing, that is, cleaning analytical laboratory errors, replacing missing values or outliers, and transforming data adequately before actual data analysis, is crucial. Because current tools available for this purpose often require programming skills, preprocessing tools with graphical user interfaces that can be used interactively are needed. In collaboration between data scientists and experts in bioanalytical diagnostics, a graphical software package for data preprocessing called pguIMP is proposed, which contains a fixed sequence of preprocessing steps to enable reproducible interactive data preprocessing. As an R‐based package, it also allows direct integration into this data science environment without requiring any programming knowledge. The implementation of contemporary data processing methods, including machine‐learning‐based imputation techniques, ensures the generation of corrected and cleaned bioanalytical data sets that preserve data structures such as clusters better than is possible with classical methods. This was evaluated on bioanalytical data sets from lipidomics and drug research using k‐nearest‐neighbors‐based imputation followed by k‐means clustering and density‐based spatial clustering of applications with noise. The R package provides a Shiny‐based web interface designed to be easy to use for non–data analysis experts. It is demonstrated that the spectrum of methods provided is suitable as a standard pipeline for preprocessing bioanalytical data in biomedical research domains. The R package pguIMP is freely available at the comprehensive R archive network (https://cran.r‐project.org/web/packages/pguIMP/index.html).