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An introduction to NMF package Version 0.20.2 Renaud Gaujoux March 6, 2014 This vignette presents the NMF package1 (Gaujoux et al. 2010), which implements a framework for Nonnegative Matrix Factorization (NMF) algorithms in R (R Development Core Team 2011). The objective is to provide an implementation of some standard algorithms, while allowing the user to easily implement new methods that integrate into a common framework, which facilitates analysis, result visualisation or performance benchmarking. If you use the package NMF package in your analysis and publications please cite: Renaud Gaujoux et al. “A ?exible R package for nonnegative matrix factorization”. In: BMC Bioinformatics 11.1 (2010), p. 367. issn: 1471-2105. doi: 10.1186/1471-2105-11-367 Note that the NMF package includes several NMF algorithms, published by di?erent authors. Please make sure to also cite the paper(s) associated with the algorithm(s) you used. Citations for those can be found in Table 1 and in the dedicated help pages ?gedAlgorithm.algorithm, e.g., ?gedAlgorithm.SNMF R. Installation: The latest stable version of the package can be installed from any CRAN repository mirror: # Install install.packages(NMF) # Load library(NMF) The NMF package is a project hosted on R-forge2. The latest development version is available from /R/?group id=649 and may be installed from there3. Support: UseRs interested in this package are encouraged to subscribe to the user mailing list (nmf-user@), which is the preferred channel for enquiries, bug reports, feature requests, suggestions or NMF-related discussions. This will enable better tracking as well as fruitful community exchange. Important: Note that some of the classes de?ned in the NMF package have gained new slots. If you need to load objects saved in versions prior 0.8.14 please use: # eg., load from some RData file load(object.RData) # update class definition object - nmfObject(object) 1/package=NMF 2/projects/nmf 3install.packages(NMF, repos = htt