To cite package ‘RUVSeq’ in publications use:

  D. Risso, J. Ngai, T. P. Speed and S. Dudoit (2014). Normalization of
  RNA-seq data using factor analysis of control genes or samples Nature
  Biotechnology, 32(9), 896-902

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{Normalization of RNA-seq data using factor analysis of control genes or samples}},
    author = {Davide Risso and John Ngai and Terence Speed and Sandrine Dudoit},
    year = {2014},
    journal = {Nature Biotechnology},
    volume = {32},
    number = {9},
    pages = {896--902},
    note = {In press},
    url = {http://www.nature.com/nbt/journal/v32/n9/full/nbt.2931.html},
  }