Please cite aroma.affymetrix as

H. Bengtsson, K. Simpson, J. Bullard & K. Hansen. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008
H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008
H. Bengtsson, P. Wirapati & T.P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics, 2009

Corresponding BibTeX entries:

  @TechReport{,
    author = {H. Bengtsson and K. Simpson and J. Bullard and K.
      Hansen},
    title = {{aroma.affymetrix}: A generic framework in {R} for
      analyzing small to very large {Affymetrix} data sets in bounded
      memory},
    institution = {Department of Statistics, University of California,
      Berkeley},
    year = {2008},
    month = {February},
    number = {745},
  }
  @Article{,
    author = {H. Bengtsson and R. Irizarry and B. Carvalho and T.P.
      Speed},
    title = {Estimation and assessment of raw copy numbers at the
      single locus level},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    pages = {759--767},
    url = {http://dx.doi.org/10.1093/bioinformatics/btn016},
  }
  @Article{,
    author = {H. Bengtsson and P. Wirapati and T.P. Speed},
    title = {A single-array preprocessing method for estimating
      full-resolution raw copy numbers from all {Affymetrix} genotyping
      arrays including {GenomeWideSNP 5 \& 6}},
    journal = {Bioinformatics},
    year = {2009},
    volume = {25},
    pages = {2149--2156},
    url = {http://dx.doi.org/10.1093/bioinformatics/btp371},
  }