To cite package ‘affy’ in publications use:

  Gautier, L., Cope, L., Bolstad, B. M., and Irizarry, R. A. 2004.
  affy---analysis of Affymetrix GeneChip data at the probe level.
  Bioinformatics 20, 3 (Feb. 2004), 307-315.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Laurent Gautier and Leslie Cope and Benjamin M. Bolstad and Rafael A. Irizarry},
    title = {affy---analysis of Affymetrix GeneChip data at the probe level},
    journal = {Bioinformatics},
    volume = {20},
    number = {3},
    year = {2004},
    issn = {1367-4803},
    pages = {307--315},
    doi = {10.1093/bioinformatics/btg405},
    publisher = {Oxford University Press},
    address = {Oxford, UK},
  }