To cite package ‘affylmGUI’ in publications use:

  Wettenhall, J. M., Simpson, K. M., Satterley, K., Smyth, G. K.
  (2006). affylmGUI: a graphical user interface for linear modeling of
  single channel microarray data. Bioinformatics 22, 897-899.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{affylmGUI}: a graphical user interface for linear modeling of single channel microarray data},
    author = {James M Wettenhall and Ken M Simpson and Keith Satterley and Gordon K Smyth},
    journal = {Bioinformatics},
    year = {2006},
    volume = {22},
    pages = {897-899},
  }