marray

marray provides a unified framework for exploratory analysis, quality assessment, and normalization of two-color cDNA microarray fluorescence intensity data.

Key Features:

• Data model: Object-oriented classes (marrayClasses) represent pre- and post-normalization intensity data across batches and expose marrayRaw and marrayNorm object types.
• Import utilities: Parsers and data ingestion functions for two-color cDNA microarray intensity datasets.
• Diagnostic visualizations: Functions for boxplots, scatterplots, MA plots, and spatial color images of spot statistics including foreground/background intensities, log-ratios, and spot area.
• Normalization algorithms: Robust adaptive location–scale normalization procedures with support for global and print-tip–specific adjustments.
• Control incorporation and bias correction: Support for incorporation of exogenous control sequences and correction of intensity-dependent dye biases, plate effects, spatial trends, and scanning irregularities.
• Interoperability: Outputs structured for integration with downstream differential expression and visualization analyses.

Scientific Applications:

• Exploratory analysis: Visual and numerical exploration of two-color microarray intensity distributions and relationships.
• Quality assessment: Detection of array-level artifacts such as printing defects, hybridization issues, spatial artifacts, and scanning irregularities.
• Normalization and bias correction: Removal of dye bias, plate effects, and spatial trends through adaptive location–scale methods and print-tip adjustments.
• Preprocessing for differential expression: Preparation of normalized intensity data suitable for downstream differential expression and statistical analyses.

Methodology:

Uses an R object-oriented class/method system (marrayClasses) with import utilities; computes diagnostic boxplots, scatterplots, MA plots, and spatial color images of spot statistics; applies robust adaptive location–scale normalization with options for global or print-tip–specific adjustments and incorporation of exogenous control sequences.