@Manual{affy4,
  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},
}

@TechReport{affy:tech:2001,
  author       = {Affymetrix},
  title        = {GeneChip Expression Analysis Algorithm Tutorial},
  year         = {2001},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2002,
  author       = {Affymetrix},
  title        = {Statistical Algorithms Description Document},
  year         = {2002},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2005,
  author       = {Affymetrix},
  title        = {GeneChip Exon Array Design},
  year         = {2005},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2005a,
  author       = {Affymetrix},
  title        = {Gene Signal Estimates from Exon Arrays},
  year         = {2005},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2005b,
  author       = {Affymetrix},
  title        = {Exon Probeset Annotations and Transcript Cluster Groupings},
  year         = {2005},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2005c,
  author       = {Affymetrix},
  title        = {Exon Array Background Correction},
  year         = {2005},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{affy:tech:2005d,
  author       = {Affymetrix},
  title        = {Quality Assessment of Exon Arrays},
  year         = {2005},
  organization = {Affymetrix},
  institution  = {Affymetrix},
}

@TechReport{root:2009,
  author       = {The ROOT team},
  title        = {{ROOT} {U}ser {G}uide},
  year         = {2009},
  organization = {CERN},
  institution  = {CERN},
  url          = {http://root.cern.ch/drupal/content/users-guide},
}

@Article{strato:2003,
  author    = {C. Stratowa},
  title     = {Distributed Storage and Analysis of Microarray Data in the Terabyte Range: An Alternative to BioConductor},
  journal   = {Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC2003)},
  year      = {2003},
  url       = {http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/Stratowa.pdf},
}

@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},
  volume    = {4},
  number    = {2},
  pages     = {249--264},
  year      = {2003},
}

@Article{bols:etal:2003,
  author  = {B.M. Bolstad and R.A. Irizarry and M. {\AA}strand and T.P. Speed},
  title   = {A comparison of normalization methods for high density oligonucleotide array data based on variance and bias},
  journal = {Bioinformatics},
  volume  = {19},
  number  = {2},
  pages   = {185--193},
  month   = {Jan},
  year    = {2003},
}

@Article{bols:2001,
  author    = {Ben Bolstad},
  title     = {Probe level quantile normalization of high density oligonucleotide arrays},
  journal   = {Unpublished manuscript},
  year      = {2001},
  OPTkey    = {},
  OPTvolume = {},
  OPTnumber = {},
  OPTpages  = {},
  OPTmonth  = {},
  OPTnote   = {},
  OPTannote = {},
}

@Article{dudo:etal:2001,
  author    = {S. Dudoit and Y. H. Yang and M. J. Callow and T. P. Speed},
  title     = {Statistical methods for identifying genes with differential expression in replicated c{DNA} microarray experiments},
  journal   = {Statistica Sinica},
  year      = {2002},
  volume    = {12},
  number    = {1},
  pages     = {111-139},
}

@Article{gaut:cope:bols:iriz:2003,
  author  = {Gautier, Laurent and Cope, Leslie and Bolstad, Benjamin Milo and Irizarry, Rafael A.},
  title   = {affy - An {R} package for the analysis of Affymetrix GeneChip data at the probe level},
  journal = {Bioinformatics},
  volume  = {20},
  number  = {3},
  pages   = {307--315},
  month   = {Feb},
  year    = {2004},
}

@Article{robin:speed:2007,
  author  = {Robinson, Mark and Speed, Terence},
  title   = {A comparison of Affymetrix gene expression arrays},
  journal = {BMC Bioinformatics},
  volume  = {8},
  number  = {449},
  pages   = {1--16},
  month   = {Nov},
  year    = {2007},
}

@Article{chen:etal:2007,
  author  = {Z. Chen and M. McGee and Q. Liu and R.H. Scheuermann},
  title   = {A distribution free summarization method for Affymetrix GeneChip arrays},
  journal = {Bioinformatics},
  volume  = {23},
  number  = {3},
  pages   = {321--327},
  month   = {Feb},
  year    = {2007},
}

@Article{hochr:etal:2006,
  author  = {S. Hochreiter and D.A. Clevert and K. Obermayer},
  title   = {A new summarization method for Affymetrix probe level data},
  journal = {Bioinformatics},
  volume  = {22},
  number  = {8},
  pages   = {943--949},
  month   = {Apr},
  year    = {2006},
}

@Article{tallo:etal:2007,
  author  = {W. Talloen and D.A. Clevert and K. Obermayer and D. Amaratunga and J. Bijnens and S. Kass and H.W.H. Gohlmann},
  title   = {I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data},
  journal = {Bioinformatics},
  volume  = {23},
  number  = {21},
  pages   = {2897--2902},
  month   = {Nov},
  year    = {2007},
}
