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Bioinformatics. 2012 Jul 1;28(13):1793-4. doi: 10.1093/bioinformatics/bts248. Epub 2012 May 9.

CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.

Author information

  • 1CEIT and TECNUN, University of Navarra, 20018 San Sebastian, Spain.

Abstract

SUMMARY:

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.

AVAILABILITY:

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/).

PMID:
22576175
[PubMed - indexed for MEDLINE]
PMCID:
PMC3381965
Free PMC Article
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