@Manual{R,
title = {R: A language and environment for statistical computing},
author = {R Development Core Team},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2005},
note = {{ISBN} 3-900051-07-0},
url = {http://www.R-project.org},
}
@Manual{AFE,
title = {Agilent Feature Extraction Reference Guide},
author = {Agilent},
year = {2007},
url = {http://www.Agilent.com},
}
@Article{RMA,
author = {R. Irizarry and B. Hobbs and F. Collin and Y. Beazer-Barclay and K. Antonellis and
U. Scherf and T. P. Speed},
title = {Exploration, normalization, and summaries of high density oligonucleotide array probe level data},
journal = {Biostatistics},
year = {2003},
volume = {4},
pages = {249-264},
}
@Article{Gentleman,
author = {R. Gentleman and V.J. Carey and D.M. Bates and B. Bolstad and M
Dettling and S. Dudoit and B. Ellis and L. Gautier and Y. Ge and others},
title = {Bioconductor: Open software development for computational biology and  bioinformatics},
journal = {Genome Biology},
year = {2004},
volume = {5},
pages = {R80},
number = {43},
}
@inbook{limma,
title = {Limma: linear models for microarray data},
author = {G. K. Smyth},
booktitle = {Bioinformatics and Computational Biology Solutions using R and Bioconductor},
editor = {R. Gentleman and  V. Carey and S. Dudoit and R. Irizarry and W. Huber},
publisher = {Springer},
address = {New York},
year = {2005},
pages = {397--420},
}
@Article{ebayes,
author = {G. K. Smyth},
title = {Linear models and empirical Bayes methods for assessing
	diferential expression in microarray experiments},
journal = { Statistical Applications in Genetics and Molecular Biology},
year = {2004},
volume = {3},
url = {http://www.bepress.com/sagmb/vol3/iss1/art3},
}
@inbook{Bold3,
title = {Quality Assesement of Affymetrix GeneChip Data},
author = {B. M. Bolstad and F. Collin and J. Brettschneider and K. Simpson and L. Cope
and R. Irizarry and T. P. Speed, T.P.},
booktitle = {Bioinformatics and Computational Biology Solutions using R and Bioconductor},
editor = {Robert Gentleman, Vincent J Carey, Wolfgang Huber, Rafael A Irizarry, Sandrine Dudoit},
publisher = {Springer},
address = {New York},
year = {2005},
pages = {397--420},
url = {http://dx.doi.org/10.1007/0-387-29362-0_3},
}
@Article{quant1,
author = {B. M. Bolstad},
title = {Probe level quantile normalization of high density oligonucleotide array data},
journal = {Unpublished Manuscript},
year = {2001},
url = {http://bmbolstad.com/stuff/qnorm.pdf},
}
@Article{quant2,
author = {B. M. Bolstad and R. Irizarry and M. Astrand and T. P. Speed},
title = {A comparison of normalization methods for high density oligonucleotide array data based on variance and bias},
journal = {Bioinformatics},
year = {2003},
volume = {19},
pages = {185-193},
}
@Article{Norm,
author = {G. K. Smyth and T. P. Speed},
title = {Normalization of cDNA microarray data},
journal = {Methods},
year = {2003},
volume = {31},
pages = {265-273},
}
@Article{affy,
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 = {http://dx.doi.org/10.1093/bioinformatics/btg405},
publisher = {Oxford University Press},
address = {Oxford, UK},
}
@Manual{preprocessCore,
title = {preprocessCore: A collection of pre-processing functions},
author = {B. M. Bolstad},
year = {},
note = {R package version 1.4.0},
}
