oligo

oligo analyzes oligonucleotide arrays at the probe level to enable preprocessing and downstream analysis of expression, SNP, tiling, and exon arrays.

Key Features:

• Probe-level analysis: Performs probe-level processing and analysis of individual probe intensities for oligonucleotide arrays.
• Support for array types: Handles expression, SNP, tiling, and exon arrays.
• File format support: Reads Affymetrix CEL files and NimbleGen XYS files for data access.
• Unified preprocessing paradigm: Implements a consistent preprocessing approach to prepare data for accurate downstream analysis.
• Integration with BioConductor tools: Interfaces with other BioConductor tools for statistical testing and visualization.
• Flexibility and generalization: Built on the BioConductor framework and adheres to principles of transparency and reproducibility to support diverse microarray technologies.

Scientific Applications:

• Gene expression analysis: Enables probe-level investigation of differential gene expression in expression arrays.
• SNP and exon array studies: Supports analysis of SNP arrays and exon arrays for genetic variation and alternative splicing investigations.
• Tiling array analysis: Applies probe-level processing to tiling arrays for genome-scale probe signal analysis.

Methodology:

Implements a unified preprocessing paradigm and extends existing preprocessing methods by leveraging established codebases for data access and visualization, using BioConductor infrastructure to read Affymetrix CEL and NimbleGen XYS files and to interface with other analysis and visualization tools.