aroma.affymetrix

aroma.affymetrix performs preprocessing and allele-specific DNA copy-number estimation for large-scale Affymetrix microarray datasets, supporting expression arrays, SNP chips, and exon arrays.

Key Features:

• Scalability: Processes Affymetrix datasets ranging from ~100 to several thousand arrays for large-scale analyses.
• Chip type support: Supports Affymetrix expression arrays, SNP chips, and exon arrays.
• ACNE integration: Integrates the ACNE (Allele-specific CN Estimation) algorithm to estimate allele-specific DNA copy numbers.
• Cross-hybridization handling: Implements methods that address cross-hybridization between alleles in SNP probe pairs.
• Allele-specific and total CN estimation: Provides estimates of both total and allele-specific copy numbers for nuanced CN analysis.
• Aberration detection: Enhances distinction between aberrant and normal genomic states for improved detection of copy-number anomalies.

Scientific Applications:

• Cancer Genomics: Precise allele-specific and total copy-number analysis to investigate tumor genomic alterations.
• Genetic Disorders: Detection of allele-specific copy-number variations relevant to monogenic and structural disorders.
• Population Genetics: Analysis of SNP data for studies of genetic diversity and population structure.

Methodology:

Integration of the ACNE algorithm for allele-specific CN estimation and computational handling of SNP probe-pair cross-hybridization to produce total and allele-specific copy-number estimates.