EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of functions two of which should be used in a sequence.
Version uploaded in March 2015 does not have Rescaling (due to a bug that is being addressed).
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 Oct 1;25(19):2573-80. doi: 10.1093/bioinformatics/btp426. Epub 2009 Jul 14.
2) "Metabolomics data normalization with EigenMS".
Submitted to PLoS ONE.
Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards L
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