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