@Article{Gautier2004,
    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 = {10.1093/bioinformatics/btg405},
    publisher = {Oxford University Press},
    address = {Oxford, UK},
}
@Manual{LeCao2015,
    title = {YuGene: A Simple Approach to Scale Gene Expression Data Derived from
Different Platforms for Integrated Analyses},
    author = {Kim-Anh {Le Cao} and Florian Rohart and Leo McHugh and Othmar Korn and Christine A. Wells},
    year = {2015},
    note = {R package version 1.1.5},
    url = {https://CRAN.R-project.org/package=YuGene},
  }
@Manual{Carlson2016,
    title = {org.Hs.eg.db: Genome wide annotation for Human},
    author = {Marc Carlson},
    year = {2016},
    note = {R package version 3.4.0},
}
@Article{Durinck2005,
    title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis},
    author = {Steffen Durinck and Yves Moreau and Arek Kasprzyk and Sean Davis and Bart {De Moor} and Alvis Brazma and Wolfgang Huber},
    journal = {Bioinformatics},
    year = {2005},
    volume = {21},
    pages = {3439--3440},
}
@article{Mah2017,
	author = {Nancy Mah and Khadija El Amrani and Weiping Zhang and Harald Stachelscheid and Andreas Kurtz},
	title = {CellFinder's Molecular Database and its Application to Stem Cell Research},
	journal = {Genomics and Computational Biology},
	volume = {3},
	number = {1},
	year = {2017},
	keywords = {},
	abstract = {CellFinder is a freely available on-line resource for cell-based data in mammalian cells and in vitro cell lines. CellFinder was developed to provide easier access to different types of cell-based data, which include anatomical and microscopic images, protein expression and whole genome mRNA expression profiles. In this short communication, we describe the collection, processing and storage of gene expression data for the CellFinder resource. Studies involving the use of normal cells and/or production of pluripotent stem cells or their engineered cell types, were chosen from public data repositories of mRNA expression data. Samples in each study were manually curated with ontology terms, and the data was further processed to yield normalized expression data. Sample, experiment and molecular data were stored in a postgreSQL database. The resulting molecular database currently contains 1588 samples from 56 studies, covering 42 cell types in human and mouse. The molecular database is undergoing continuous development and will serve as a source of standardized, processed and expertly annotated data for CellFinder analysis tools such as MarkerTool and CompareTool.},
	issn = {2365-7154},
	pages = {e48},
	doi = {10.18547/gcb.2017.vol3.iss1.e48},
	url = {https://genomicscomputbiol.org/ojs3/GCB/article/view/25}
}
@MANUAL{Team2007,
  title = {R: A Language and Environment for Statistical Computing},
  author = {R Development Core Team},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2007},
  note = {{ISBN} 3-900051-07-0},
  owner = {Schmidberger},
  timestamp = {2007.08.28},
  url = {http://www.R-project.org}
}
@Article{Irizarry2003,
	author = {Irizarry, Rafael A. and Hobbs, Bridget and Collin, Francois and Beazer--Barclay, Yasmin D. and Antonellis, Kristen J. and Scherf, Uwe and Speed, Terence P.}, 
	title = {Exploration, normalization, and summaries of high density oligonucleotide array probe level data},
	volume = {4}, 
	number = {2}, 
	pages = {249--264}, 
	year = {2003}, 
	doi = {10.1093/biostatistics/4.2.249}, 
	url = {http://biostatistics.oxfordjournals.org/content/4/2/249.abstract}, 
	journal = {Biostatistics} 
}
@Article{McCall2010,
	author = {McCall, Matthew N. and Bolstad, Benjamin M. and Irizarry, Rafael A.},
	title = {Frozen robust multiarray analysis (fRMA)},
	journal = {Biostatistics},
	volume = {11},
	number = {2},
	pages = {242-253},
	year = {2010},
	doi = {10.1093/biostatistics/kxp059},
	URL = {http://dx.doi.org/10.1093/biostatistics/kxp059}
}
@Article{Johnson2007,
	author = {Johnson, W. Evan and Li, Cheng and Rabinovic, Ariel},
	title = {Adjusting batch effects in microarray expression data using empirical Bayes methods},
	journal = {Biostatistics},
	volume = {8},
	number = {1},
	pages = {118-127},
	year = {2007},
	doi = {10.1093/biostatistics/kxj037},
	URL = {http://dx.doi.org/10.1093/biostatistics/kxj037}
}
@Article{Kauffmann2009,
	author = {Kauffmann, Audrey and Gentleman, Robert and Huber, Wolfgang},
	title = {arrayQualityMetrics—a bioconductor package for quality assessment of microarray data},
	journal = {Bioinformatics},
	volume = {25},
	number = {3},
	pages = {415-416},
	year = {2009},
	doi = {10.1093/bioinformatics/btn647},
	URL = {http://dx.doi.org/10.1093/bioinformatics/btn647}
}
