
@article{bhat_single_2009,
	title = {Single molecule detection in nanofluidic digital array enables accurate measurement of {DNA} copy number},
	volume = {394},
	issn = {1618-2650},
	doi = {10.1007/s00216-009-2729-5},
	abstract = {Digital polymerase chain reaction (PCR) is a promising technique for estimating target DNA copy number. PCR solution is distributed throughout numerous partitions, and following amplification, target DNA copy number is estimated based on the proportion of partitions containing amplified DNA. Here, we identify approaches for obtaining reliable digital PCR data. Single molecule amplification efficiency was significantly improved following fragmentation of total DNA and bias in copy number estimates reduced by analysis of short intact target DNA fragments. Random and independent distribution of target DNA molecules throughout partitions, which is critical to accurate digital PCR measurement, was demonstrated by spatial distribution analysis. The estimated relative uncertainty for target DNA concentration was under 6\% when analyzing five digital panels comprising 765 partitions each, provided the panels contained an average of 212 to 3,365 template molecules. Partition volume was a major component of this uncertainty estimate. These findings can be applied to other digital PCR studies to improve confidence in such measurements.},
	language = {eng},
	number = {2},
	journal = {Analytical and bioanalytical chemistry},
	author = {Bhat, Somanath and Herrmann, Jan and Armishaw, Paul and Corbisier, Philippe and Emslie, Kerry R},
	month = may,
	year = {2009},
	pmid = {19288230},
	keywords = {Computer Simulation, DNA, Gene Dosage, Microfluidics, Oligonucleotide Array Sequence Analysis},
	pages = {457--467}
}

@article{dube_mathematical_2008,
	title = {Mathematical analysis of copy number variation in a {DNA} sample using digital {PCR} on a nanofluidic device},
	volume = {3},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0002876},
	abstract = {Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics. We also provide formulas which can be used as close approximations.},
	language = {eng},
	number = {8},
	journal = {PloS one},
	author = {Dube, Simant and Qin, Jian and Ramakrishnan, Ramesh},
	year = {2008},
	pmid = {18682853 PMCID: PMC2483940},
	keywords = {Algorithms, Confidence Intervals, DNA, Genetic, Genetic Variation, Genome, Human, Humans, Models, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction},
	pages = {e2876}
}

@Article{roediger2015r,
  Title                    = {R as an Environment for the Reproducible Analysis of DNA Amplification Experiments},
  Author                   = {R{\"o}diger, Stefan and Burdukiewicz, Micha{\l} and Blagodatskikh, Konstantin and Schierack, Peter},
  Journal                  = {The R Journal},
  Year                     = {2015},
  Number                   = {2},
  Pages                    = {127--150},
  Volume                   = {7}
}

@Article{brown_2001,
  Title                    = {Interval Estimation for a Binomial Proportion},
  Author                   = {Brown, Lawrence D. and Cai, T. Tony and DasGupta, Anirban},
  Journal                  = {Statist. Sci.},
  Year                     = {2001},

  Month                    = {May},
  Number                   = {2},
  Pages                    = {101--133},
  Volume                   = {16},

  Doi                      = {10.1214/ss/1009213286},
  Fjournal                 = {{Statistical Science}},
  Publisher                = {The Institute of Mathematical Statistics},
  Url                      = {http://dx.doi.org/10.1214/ss/1009213286}
}