spikeLI

spikeLI analyzes Affymetrix high-density oligonucleotide microarray hybridization data by relating probe signal intensities to RNA/DNA duplex hybridization free energies, considering both perfect-match and mismatch probes, to interpret microarray results and assess probe performance.

Key Features:

• Physical hybridization model: Uses a simple physical model of the hybridization process to analyze controlled microarray experiments.
• Intensity–energy mapping: Relates probe signal intensities to RNA/DNA duplex hybridization free energies.
• Probe type handling: Explicitly models both perfect-match and mismatch probes.
• Langmuir adsorption consistency: Demonstrates that intensity–energy relationships collapse onto a single master curve consistent with Langmuir adsorption theory.
• Target–target hybridization correction: Accounts for reduction in effective target concentration caused by target–target hybridization in solution.
• Annotation diagnostics: Identifies deviations from expected thermodynamic behavior that reveal annotation problems, such as probes not complementing intended RNA targets due to outdated or incorrect database information.
• Thermodynamic parameters: Employs RNA/DNA free energy parameters to improve the stability and quality of empirical fits.
• Benchmark datasets: Examines publicly available Latin square datasets.

Scientific Applications:

• Microarray interpretation: Provides a physically grounded framework for interpreting Affymetrix high-density microarray data.
• Probe performance assessment: Assesses probe performance and the stability of empirical fits using RNA/DNA free energy modeling.
• Annotation quality control: Detects probes whose surface-bound sequences do not match intended RNA targets, indicating outdated or incorrect database annotations.
• Solution hybridization analysis: Quantifies effects of target–target hybridization in solution on effective target concentration and signal intensities.

Methodology:

Applies a simple physical hybridization model relating probe signal intensities to RNA/DNA duplex hybridization free energies (including perfect-match and mismatch probes), fits intensity–energy relationships against Langmuir adsorption theory while accounting for effective concentration reduction from target–target hybridization in solution, and evaluates results using Latin square datasets.