Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale...

Area of Science:

• Biotechnology
• Bioinformatics
• Clinical Research

Background:

• Clinical research results can be influenced by biases, particularly in sample distribution before biochemical preparation.
• High-throughput mass spectrometry (e.g., proteomics, metabolomics) requires careful experimental design to ensure data integrity.

Purpose of the Study:

• To introduce Well Plate Maker, a user-friendly application for designing single- or multiple-well plate assays.
• To provide a tool that aids in randomizing experiments and reducing potential batch effects and other sources of bias.

Main Methods:

• Well Plate Maker is implemented in R and accessible via the Bioconductor repository.
• The application features a graphical user interface developed with Shiny technology, alongside classical scripting options.

Main Results:

• The software facilitates the design of randomized experiments, helping to mitigate bias in sample distribution.
• It offers features to limit edge-of-plate effects, incorporate control samples, and minimize cross-contamination.

Conclusions:

• Well Plate Maker is a versatile tool for optimizing experimental design in various scientific fields, especially those employing high-throughput assays.
• Its user-friendly interface and randomization capabilities enhance the reliability and reproducibility of biochemical and clinical research data.