Normalyzer

Version: 1.1.1

Website

http://normalyzer.immunoprot.lth.se/normalize.php

Description

This R package is designed to evaluate the suitability of different normalisation methods for a dataset that is normally distributed, in a tab separated file with intensities. 12 different normalisation methods are evaluated: total intensity (TI), median intensity (MedI), average intensity (AI), quantile, NormFinder (NF), variance stabilising normalisation (VSN), robust linear regression (RLR) and LOESS are all global normalisation methods; VSN, RLR and LOESS are also implemented as local methods, where within replicate groups are normalised separately. These different normalisation techniques are then evaluated using many methods including: total intensity, total missing values, pooled intragroup coefficient of variation (PCV) and pearson's and spearman's correlation. The results of these evaluations are then outputted in a report. It is specifically designed for proteomics and DNA microarray and has not been tested for metabolomics by the authors.

Functionality

• Post-processing

Instrument Data Type

Approaches

• DNA microarray
• Metabolomics
• Proteomics

Computer Skills

Advanced

Software Type

• R Package

Interface

• Command line Interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

R (≥ 3.0.0), vsn, Rcmdr, PerformanceAnalytics, preprocessCore, limma, MASS, abind, e1071, ape, car, raster

Input Formats - Open

Tab-seperated format

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2015

License

GPL, Creative Commons

Paper

http://www.ncbi.nlm.nih.gov/pubmed/24766612

PMID

24766612