To cite the ffpe package in publications use the following.

  Waldron L1, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT,
  Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR,
  Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS,
  Parmigiani G, and Huttenhower C. (2012). Expression profiling of
  archival tumors for long-term health studies, Clinical Cancer
  Research, 18(22) 6136-46.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Expression profiling of archival tumors for long-term health studies},
    author = {{Waldron, L} and {Ogino, Shuji} and {Hoshida, Yujin} and {Shima, Kaori} and {McCart Reed, Amy E} and {Simpson, Peter T} and {Baba, Yoshifumi} and {Nosho, Katsuhiko} and {Segata, N} and {Vargas, Ana Cristina} and {Cummings, Margaret C} and {Lakhani, Sunil R} and {Kirkner, Gregory J} and {Giovannucci, Edward} and {Quackenbush, John} and {Golub, Todd R} and {Fuchs, Charles S} and {Parmigiani, G} and {Huttenhower, C}},
    year = {2012},
    journal = {Clinical Cancer Research},
    volume = {18},
    number = {22},
    doi = {10.1158/1078-0432.CCR-12-1915},
    note = {PMID: 23136189},
    pages = {6136--6146},
  }