affy

affy performs probe-level analysis of Affymetrix GeneChip oligonucleotide array data to support genomic and transcriptomic studies, cross-species probe selection, creation of species-specific CDFs, and identification of single-feature polymorphisms (SFPs).

Key Features:

• Probe-Level Data Analysis: Imports and analyzes Affymetrix GeneChip probe-level (CEL) data for detailed examination of probe signals.
• Cross-Species Application: Supports genomic DNA–based probe selection and analysis for heterologous (Xspecies) studies using high-density oligonucleotide arrays.
• Customization and Flexibility: Enables empirical determination of probe-quality boundaries for removing poor probes and the creation of species-specific Chip Description Files (CDFs).
• Identification of Single-Feature Polymorphisms (SFPs): Examines experimental designs to identify potential SFPs at both DNA and RNA levels.
• Visualization and Interactive Analysis: Provides visualization and interactive analysis capabilities for exploration of microarray datasets.

Scientific Applications:

• Genomic and Transcriptomic Studies: Supports gene expression analysis and genetic variation studies in both model and non-model species using microarray data.
• Cross-Species Research: Facilitates analysis of heterologous species and underutilized organisms through genomic DNA–based probe selection and species-adapted probe sets.
• Custom Experimental Design: Enables tailored experimental designs by identifying SFPs and customizing probe sets and CDF files for specific species.

Methodology:

Import Affymetrix GeneChip probe-level data; determine empirical probe-quality thresholds from hybridization results; generate species-specific CDF files; analyze experimental designs to identify potential SFPs at DNA and RNA levels.