@InBook{iriz:gaut:cope:2003,
  author =	 {Rafael A. Irizarry and Laurent Gautier and Leslie M. Cope},
  editor =	 {Parmigiani, G. and Garrett, E.S. and Irizarry, R.A. and Zeger, S.L.},
  title = 	 {The Analysis of Gene Expression Data: Nethods and Software},
  chapter = 	 {4},
  publisher = 	 {Spriger Verlag},
  year = 	 {2003},
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  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTpages = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}
@InBook{dudo:2002,
  author =	 {Sandrine Dudoit},
  editor =	 {Parmigiani, G. and Garrett, E.S. and Irizarry, R.A. and Zeger, S.L.},
  title = 	 {The Analysis of Gene Expression Data: Nethods and Software},
  chapter = 	 {3},
  publisher = 	 {Spriger Verlag},
  year = 	 {2002},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTpages = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InBook{gent:care:2002,
  author =	 {Robert Gentleman and Vince Carey},
  editor =	 {Parmigiani, G. and Garrett, E.S. and Irizarry, R.A. and Zeger, S.L.},
  title = 	 {The Analysis of Gene Expression Data: Nethods and Software },
  chapter = 	 {2},
  publisher = 	 {Springer Verlag},
  year = 	 {2002},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTpages = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{ihak:gent:1996,
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@Book{cham:1998,
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@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},
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  year = 	 {2003},
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  note =	 {To appear},
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}

@Manual{affy4,
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  edition =	 {version 4},
}

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

@Article{hill:etal:2000,
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@Article{hill:etal:2001,
  author = 	 {Andre A. Hill and Eugene L. Brown and Maryann Z. Whitley and Greg Tucker-Kellogg and Craig P. Hunter and Donna K. Slonim},
  title = 	 {Evaluation of normalization procedures for oligonucleotide array data based on spiked c{RNA} controls},
  journal = 	 {Genomebiology},
  year = 	 {2001},
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@Article{baug:etal:2001,
  author = 	 {L.R. Baugh and A.A. Hill and E.L. Brown and Craig P. Hunter},
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  volume =	 {29},
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  pages =	 {1--9},
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}

@TechReport{affy:tech:2001,
  author = 	 {Affymetrix},
  title = 	 {New Statistical Algorithms for Monitoring Gene Expression on $\mbox{GeneChip}^{\mbox{\textregistered}}$ Probe Arrays},
  institution =  {Affymetrix},
  year = 	 {2001},
}

@techreport{affy:tech:2002,
key = {Affymetrix (2002)},
author = {Affymetrix},
title = {Statistical Algorithms Description Document},
organization = {Affymetrix},
institution = {Affymetrix},
year = 2002
}

@InProceedings{affytalk:2001,
   title = 	 {Estimating Signal with Next Generation {A}ffymetrix Software},
  author = 	 {Earl Hubbell},
booktitle = 	 {Gene Logic Workshop on Low Level Analysis of Affymetrix $\mbox{GeneChip}^{\mbox{\textregistered}}$ data},
  year =	 {2001},
  note =	 {{\small \tt http://www.stat.berkeley.edu/users/terry/zarray/Affy/GL\_Workshop/genelogic2001.html}}
}

@InProceedings{fang:li:wong:2001,
   title = 	 {Model-based Saturation Handling},
  author = 	 {Xuemin Fang and Cheng Li and Wing Hung Wong},
booktitle = 	 {Genelogic Workshop on Low Level Analysis of Affymetrix $\mbox{GeneChip}^{\mbox{\textregistered}}$ data},
  year =	 {2001},
  note =	 {{\small \tt http://www.stat.berkeley.edu/users/terry/zarray/Affy/GL\_Workshop/genelogic2001.html}}
}


@InProceedings{hold:etal:2001,
  author = 	 {Daniel Holder and Richard F. Raubertas and V. Bill Pikounis and Vladimir Svetnik and Keith Soper},
  title = 	 {Statistical analysis of high density oligonucleotide arrays: a {SAFER} approach},
    year = 	 {2001},
  booktitle = 	 {Proceedings of the ASA Annual Meeting, Atlanta, GA 2001},
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  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTorganization = {},
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  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{astr:2001,
  author = 	 {Magnus {\AA}strand},
  title = 	 {Normalizing oligonucleotide arrays},
  journal = 	 {Unpublished manuscript},
  year = 	 {2001},
  OPTkey = 	 {},
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  OPTnote = 	 {},
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}

@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 = 	 {},
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}

@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
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  journal =      {Statistica Sinica},
  year =         {2001},
  OPTkey =       {},
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  OPTnumber =    {},
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  note =	 {Accepted},
  OPTannote =    {}
}

@Article{li:wong:2001a,
   Author = {Li, C. and Wong, W.H.},
   Title = {Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection},
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   Pages = {31--36},
} 

@Article{li:wong:2001b,
   Author = {Li, C. and Wong, W.H.},
   Title = {Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application},
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   Year = 2001,
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} 

@Article{lock:etal:1996,
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@InProceedings{hart:etal:2001,
  author = 	 {Alexander J. Hartemink and David K. Gifford and Tommi S. Jaakola and Richard A. Young},
  title = 	 {Maximum likelihood estimation of optimal scaling factors for expression array normalization},
  booktitle = 	 {SPIE BiOS},
  year =	 2001,
  month =	 {January},
  annote =	 {affymetrix, high density oligonucleotide}
}




@Article{efro:etal:2001,
   Author = {Bradley Efron and Robert Tibshirani and Virginia Goss and Gil Chu},
   Title = {Microarrays and their uses in comparative experiments},
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} 

@Article{naef:etal:2001,
   Author = {F\'{e}lix Naef and Daniel A. Lim and Nila Patil and Marcelo O. Magnasco},
   Title = {From features to expression: High density oligonucleotide array analysis revisited},
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   Year = 2001,
   Volume = {1},
   Pages = {1--9}
} 



@Article{astr:2003,
  author = 	 {Magnus {\AA}strand},
  title = 	 {Contrast Normalization of Oligonucleotide Arrays},
  journal = 	 {Journal of Computational Biology},
  year = 	 {2003},
volume = {10},
number={1},
pages={95--102}
}

@article{Dudoit:2002,
author = {Dudoit, S. and  Yang, Y. H. and  Callow, M. J. and Speed, T. P.},
title = {Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments},
journal = {Stat. Sin.},
year = 2002,
volume = 12,
number = 1,
pages={111-139}
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@Article{workman:etal:2002,
   Author="Workman, Christopher. and Jensen, Lars. Juhl. and Jarmer, Hanne. and Berka, Randy. and Gautier, Laurent. and Nielser, Henrik. Bjorn. and Saxild, Hans.-Henrik and Nielsen, Claus. and Brunak, Soren. and Knudsen, Steen.",
   Title="{A new non-linear normalization method for reducing variability in DNA microarray experiments}",
   Journal="Genome Biol",
   Year="2002",
   Volume="3",
   Number="9",
   Pages="research0048",
   Month="Aug"
}


@Article{Lazardis:etal:2002,
   Author="Lazaridis, Emmanuel. N. and Sinibaldi, Dominic. and Bloom, Gregory. and Mane, Shrikant. and Jove, Richard.",
   Title="{A simple method to improve probe set estimates from oligonucleotide arrays}",
   Journal="Math Biosci",
   Year="2002",
   Volume="176",
   Number="1",
   Pages="53-58",
   Month="Mar"
}


@Book{Tukey:1977,
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@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},
   note={In press},  
 Year ={2003},
}

