symbioticMe/proBatch: Tools for Batch Effects Diagnostics and Correction

The proBatch package facilitates batch effects analysis and correction in high-thoughput experiments. Although the package has primarily been developed for mass-spectrometry proteomics (DIA/SWATH), it should also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Diagnostics part of the package features unified color scheme for plotting, that allows to produce publication-quality graphs. Correction functions are convenient wrappers for common normalization and batch effects removal approaches such as quantile normalizetion and median centering. Furthermore, the package includes non-linear fitting based approaches to deal with complex, mass spectrometry-specific signal drifts. Quality control step, mostly based on correlation analysis, allows to assess whether the correction improved the quality of the data. All steps of batch effects analysis and correction are illustrated in the vignette, using the subset of real-world large-scale dataset.

Getting started

Package details

AuthorJelena Cuklina <[email protected]>, Chloe H. Lee <[email protected]>, Patrick Pedrioli <[email protected]>
Bioconductor views BatchEffect MassSpectrometry Normalization Preprocessing Proteomics QualityControl Software
MaintainerThe package maintainer Jelena Cuklina <[email protected]>
LicenseGPL-3
Version0.99.3
URL https://github.com/symbioticMe/proBatch
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("symbioticMe/proBatch")
symbioticMe/proBatch documentation built on Jan. 3, 2019, 4:17 p.m.