@article{ihak:gent:1996,
  author =    {Ross Ihaka and Robert Gentleman},
  title =     {{R}: {A} Language for Data Analysis and Graphics},
  journal =   {Journal of Computational and Graphical Statistics},
  year =      1996,
  volume =    5,
  number =    3,
  pages =     {299--314}
}

@Book{cham:1998,
  author =	 {John M. Chambers},
  title = 	 {Programming with Data: A guide to the {S} language},
  publisher = 	 {Springer},
  year = 	 {1998},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  annote =	 {S, Programming}
}

@Article{iriz:etal:2003,
  author = {Rafael A. Irizarry and Bridget Hobbs and Francois Collin and Yasmin D. Beazer-Barclay and Kristen J. Antonellis and Uwe Scherf and Terence P. Speed},
  title = 	 {Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data},
  journal = 	 {Biostatistics},
  year = 	 {2003},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  note =	 {To appear},
  OPTannote = 	 {}
}

@Article{hochreiter:etal:2006,
  author = {Sepp Hochreiter and  Djork-Arne Clevert and Klaus Obermayer},
  title = 	 {A new summarization method for affymetrix probe level data},
  journal = 	 {Bioinformatics},
  year = 	 {2006},
  OPTkey = 	 {},
  OPTvolume = 	 {22},
  OPTnumber = 	 {},
  OPTpages = 	 {943-949},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}

@Article{luo:etal:2009,
  author =       {Luo, Weijun and Friedman, Michael and Shedden, Kerby and Hankenson, Kurt and Woolf, Peter},
  title = 	 {{GAGE}: generally applicable gene set enrichment for pathway analysis},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  OPTvolume = 	 {10},
  OPTnumber = 	 {1},
  OPTpages = 	 {161},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}


@Article{luo:etal:2013,
  author =       {Luo, Weijun and Brouwer, Cory},
  title = 	 {{Pathview: an R/Bioconductor package for pathway based data integration and visualization}},
  journal = 	 {submitted},
  year = 	 {2013},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}

@Article{kim:etal:2005,
  author =       {Kim, SY and Volsky, DJ},
  title = 	 {{PAGE}: parametric analysis of gene set enrichment},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2005},
  OPTkey = 	 {},
  OPTvolume = 	 {6},
  OPTnumber = 	 {},
  OPTpages = 	 {144},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}

@Article{subra:etal:2005,
  author =       {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.},
  title = 	 {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles},
  journal = 	 {Proceedings of the National Academy of Sciences of the United States of America},
  year = 	 {2005},
  OPTkey = 	 {},
  OPTvolume = 	 {102},
  OPTnumber = 	 {43},
  OPTpages = 	 {15545-15550},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}

@Article{emery:etal:2009,
  author =       {Lyndsey A. Emery and Anusri Tripathi and Chialin King and Maureen Kavanah and Jane Mendez and Michael D. Stone and Antonio de las Morenas and Paola Sebastiani and Carol L. Rosenberg},
  title = 	 {Early Dysregulation of Cell Adhesion and Extracellular Matrix Pathways in Breast Cancer Progression},
  journal = 	 {The American journal of pathology},
  year = 	 {2009},
  OPTkey = 	 {},
  OPTvolume = 	 {175},
  OPTnumber = 	 {},
  OPTpages = 	 {1292-1302},
  OPTmonth = 	 {},
  note =	 {},
  OPTannote = 	 {}
}


  title = 	 {Affymetrix Microarray Suite User Guide},
author = {Affymetrix},
year = {1999},
  organization = {Affymetrix},
  address =	 {Santa Clara, CA},
  edition =	 {version 4},
}

@Manual{affy5,
  title = 	 {Affymetrix Microarray Suite User Guide},
author = {Affymetrix},
year = {2001},
  organization = {Affymetrix},
  address =	 {Santa Clara, CA},
  edition =	 {version 5},
}

