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aroma.affymetrix is an R package for the analysis of Affymetrix data to detect copy number variation (CNV). The aroma.affymetrix algorithm computes an unbiased reference signal from the test samples using publicly available reference sets in an attempt to eliminate an in-house reference.


Genetics; ChIP-seq; DNA polymorphism; Population genetics


  • Operation: Expression data rendering; Gene expression analysis; Variation detection
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 3.2.0
  • Maturity: Stable
  • Credit: The American Cancer Society, the National Institutes of Health, the St. Baldrick's Foundation, the National Childhood Cancer Foundation.
  • Contact: Robert W Sobol rws9 _at_
  • Collection: Aroma


Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboise WA, Brown AR, Jakacki RI, Pollack IF, Sobol RW "A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples." BMC Med Genomics. 2011 Jan 26;4:14.
PMID: 21269491
PMCID: PMC3041647

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