EigenMS

EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence.

Please download EigenMS.zip file (latest version).

Latest version uploaded in October 2017 has a bugfix for single treatment group normalization.
Rescaling has been omitted from 2015.

EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be utilized for any -omic platform.

We have shown its utility in LC-MS/MS and metabolomics in the following two papers:

1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition".
Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR.
Bioinformatics 2009

2) "Metabolomics data normalization with EigenMS"
Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM.
PLoS One 2014

Project Activity

See All Activity >

License

GNU General Public License version 2.0 (GPLv2), GNU General Public License version 3.0 (GPLv3)

Follow EigenMS

EigenMS Web Site

Other Useful Business Software

Gen AI apps are built with MongoDB Atlas

The database for AI-powered applications.

MongoDB Atlas is the developer-friendly database used to build, scale, and run gen AI and LLM-powered apps—without needing a separate vector database. Atlas offers built-in vector search, global availability across 115+ regions, and flexible document modeling. Start building AI apps faster, all in one place.

Start Free

Rate This Project

User Reviews

Be the first to post a review of EigenMS!

Additional Project Details

Intended Audience

Science/Research

Programming Language

MATLAB, S/R

Related Categories

MATLAB Bio-Informatics Software, S/R Bio-Informatics Software

Registered

2009-01-18

Similar Business Software

Bioconductor

The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists. Resources to maximize the potential of Bioconductor. From basic functionalities to...

See Software
Metabolon

At Metabolon, we offer the largest Level 1 library in the metabolomics industry. Our proprietary library has been built and curated over 20 years and contains over 5,400 entries. The vast majority of entries in our library are Level 1 attributing approximately 85% (~4,600 entries); however, some...

See Software
Cellenics

Turn your single-cell RNA sequencing data into meaningful insight with Cellenics software. Biomage hosts a community instance of Cellenics, an open source analytics tool for single-cell RNA sequencing data that has been developed at Harvard Medical School. It enables biologists to explore...

See Software
Evo 2

Evo 2 is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It utilizes a frontier deep learning architecture to model biological sequences at single-nucleotide resolution, achieving near-linear scaling of compute and memory relative to...

See Software
Loupe Browser

Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze your 10x Genomics Chromium and Visium data. You can also convert your Seurat objects into Loupe Browser files using the LoupeR package. The navigation and interactive...

See Software
MEGA

MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis...

See Software