batchCorr

Version: 0.1.9

Website

https://gitlab.com/CarlBrunius/batchCorr

Description

This is designed for between and within-batch correction of LC-MS data. There are functions for batch alignment, drift correction and batch normalisation. For batch alignment feature missingness is aggregated on a batch level, features with missingness that are sufficiently similar m/z and retention time and ensuring orthogonal batch presence among feature alignment candidates. Drift correction is performed using clustering (mclust) on features in observation space. It provides a trade-off between the power per drift pattern and the multiple drift patterns within the dataset. For batch normalisation either QC/Reference or population (median) normalisation can be used. A quality heuristic is used to determine whether the QC/Reference is suitable for normalisation; if it is not, median normalisation is used instead.

Functionality

• Post-processing

Instrument Data Type

• MS/LC-MS

Approaches

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 2.10)

Input Formats - Open

Peaklist, xcmsSet

Input Formats - Proprietary

N/A

Published

2016

Last Updated

2017

License

GPL-2

Paper

http://www.ncbi.nlm.nih.gov/pubmed/27746707

PMID

27746707