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.

Corresponding BibTeX entry:

  @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},
  }