Please cite the relevant papers for individual methods and the missMethyl Bioinformatics paper for the whole package.

Maksimovic, J.,Gordon, L., and Oshlack, A. (2012). SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biology 13(6), R44

Phipson, B., and Oshlack, A. (2014). DiffVar: A new method for detecting differential variability with application to methylation in cancer and aging. Genome Biology 15(9), 465.

Maksimovic, J., Gagnon-Bartsch, J.A., Speed, T.P., and Oshlack, A. (2015). Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data. Nucleic acids research, gkv526.

Phipson, B., Maksimovic, J., and Oshlack, A. (2015). missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450 platform. Bioinformatics, btv560.

Corresponding BibTeX entries:

  @Article{,
    author = {Jovana Maksimovic and Lavinia Gordon and Alicia Oshlack},
    title = {SWAN: Subset-quantile within array normalization for
      illumina infinium HumanMethylation450 BeadChips},
    journal = {Genome Biology},
    volume = {13},
    number = {6},
    pages = {R44},
    year = {2012},
  }

  @Article{,
    author = {Belinda Phipson and Alicia Oshlack},
    title = {DiffVar: A new method for detecting differential
      variability with application to methylation in cancer and aging},
    journal = {Genome Biology},
    volume = {15},
    number = {9},
    pages = {465},
    year = {2014},
  }

  @Article{,
    author = {Jovana Maksimovic and Johann A Gagnon-Bartsch and Terence
      P Speed and Alicia Oshlack},
    title = {Removing unwanted variation in a differential methylation
      analysis of Illumina HumanMethylation450 array data},
    journal = {Nucleic acids research},
    pages = {gkv526},
    year = {2015},
  }

  @Article{,
    author = {Belinda Phipson and Jovana Maksimovic and Alicia
      Oshlack},
    title = {missMethyl: an R package for analysing methylation data
      from Illuminas HumanMethylation450 platform},
    journal = {Bioinformatics},
    pages = {btv560},
    year = {2015},
  }