ProbePlus

ProbePlus analyzes Affymetrix GeneChip® Gene Expression Array data at the probe level to quantify probe hybridization and support detailed gene expression analysis.

Key Features:

• Probe-Level Analysis: Operates directly on individual probe intensities rather than aggregated gene-level summaries.
• PM and MM Integration: Integrates Perfect Match (PM) and Mis-match (MM) intensities for each probe pair within a probe set to inform quantification.
• Gene Expression Index (GEI) Generation: Computes a Gene Expression Index (GEI) from integrated probe intensities across probe pairs in a probe set.
• Optional Probe-Level Quantification: Supports analysis workflows that bypass GEI generation, enabling direct probe-level investigations.
• Generalized Probe Models (GPM) Support: Implements the principles of Generalized Probe Models to accommodate diverse probe measures.
• Comparative Framework for Summarization Methods: Facilitates comparisons across methods such as MAS 5.0, dChip, and RMA when the same probe measures are used.

Scientific Applications:

• Differential Gene Expression Analysis: Enables detection and characterization of differential expression from Affymetrix GeneChip probe-level data.
• Probe Hybridization Quantification: Provides detailed assessment of probe hybridization behavior using PM and MM intensity integration.
• Method Comparison and Validation: Supports evaluation and comparison of summarization methods (MAS 5.0, dChip, RMA) under consistent probe-measure choices.

Methodology:

Implements Generalized Probe Models (GPMs) that use PM and MM probe intensities to compute probe measures and optionally generate a Gene Expression Index (GEI).