proBatch

proBatch facilitates batch effects analysis and correction in high-throughput experiments, with particular utility for mass-spectrometry proteomics (DIA/SWATH) and adaptability to most omic data types.

Key Features:

• Diagnostics: Provides proteome/genome-wide and feature-level diagnostic functions for assessing batch effects.
• Correction: Implements normalization and batch effects correction methods.
• Quality Control: Includes techniques to control and evaluate batch effect adjustment quality.
• Non-linear Fitting: Incorporates non-linear fitting based approaches to address complex, mass spectrometry-specific signal drifts.
• Missing Value Handling: Addresses missing values in quantitative feature matrices specific to proteomic challenges.

Scientific Applications:

• Mass Spectrometry Proteomics: Supports DIA/SWATH and other large-scale proteomic studies encompassing hundreds of samples with multiple experimental designs.
• Clinical Proteomics: Enables robust extraction of true biological signal for reliable and reproducible research in clinical settings.
• Systems Biology: Facilitates transparent analysis workflows for systems biology investigations involving large sample sets.
• Cross-Omic Analysis: Applicable with minor adaptations to most omic data types beyond proteomics.

Methodology:

The package implements established methodologies from related fields alongside solutions specific to proteomic challenges such as ion intensity drift and missing values in quantitative feature matrices, with non-linear fitting approaches for mass spectrometry-specific signal drifts.