CAFE

CAFE detects and visualizes gross chromosomal aberrations from Affymetrix expression microarray (*.CEL) data by identifying deviations in expression profiles.

Key Features:

• Detection: Identifies gross chromosomal aberrations from expression microarray data.
• Input format: Processes Affymetrix *.CEL files (raw gene expression data) from Affymetrix arrays.
• Implementation: Implemented as an R package.
• Visualization: Provides flexible plotting functions for visualization of chromosomal abnormalities.
• Analytical approach: Leverages comprehensive expression profiles to identify deviations indicative of chromosomal aberrations.

Scientific Applications:

• Cancer genomics: Detection and visualization of chromosomal aberrations associated with tumor genomes.
• Genetic disorders: Analysis of expression-derived chromosomal abnormalities relevant to genetic disorders.
• Genomic research: Application in studies of other conditions where gross chromosomal aberrations play a role.

Methodology:

Implemented as an R package that processes Affymetrix *.CEL expression microarray files, analyzes expression profiles to identify deviations indicative of gross chromosomal aberrations, and generates flexible plots for visualization.