title: CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
abstract: CONCLUSIONS
  CalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.
  
  
  BACKGROUND
  The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project.org/).
authors.affiliation: CEIT and TECNUN, University of Navarra, 20018 San Sebastian, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Ortiz-Estevez
authors.forename: Ander
authors.initials: A
authors.lastname: Aramburu
authors.forename: Henrik
authors.initials: H
authors.lastname: Bengtsson
authors.forename: Pierre
authors.initials: P
authors.lastname: Neuvial
authors.forename: Angel
authors.initials: A
authors.lastname: Rubio
mesh_terms: D000483:Alleles; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software