matchBox

matchBox compares ranked vectors of gene expression features from microarray data to support cross-platform and inter-laboratory analysis, dataset integration, redundancy removal, visualization (CAT-plots and Venn diagrams), and statistical assessment of RNA expression.

Key Features:

• Comparison of Ranked Vectors: Compares ranked vectors of gene expression features derived from microarray experiments for nuanced concordance analysis.
• Merging Multiple Datasets: Integrates multiple microarray datasets to enable meta-analysis and cross-platform comparisons.
• Redundancy Removal: Identifies and removes redundant features to streamline feature sets prior to downstream analysis.
• Visualization Tools: Generates CAT-plots and Venn diagrams to visualize overlaps and differences among feature lists.
• Statistical Significance Computation: Applies statistical methods to assess the significance of observed patterns and agreements in expression data.

Scientific Applications:

• Microarray RNA Expression Analysis: Facilitates analysis of high-throughput RNA expression measured by microarray across thousands of genes.
• Cross-Platform Comparisons: Enables identification of consistencies and discrepancies in gene expression across different microarray platforms.
• Inter-Laboratory Assessments: Supports assessment of inter-laboratory variability when identical RNA samples are measured across laboratories.

Methodology:

Computationally compares ranked vectors, merges datasets, removes redundant features, computes statistical significance, and produces CAT-plots and Venn diagrams; development was informed by a consortium study comparing three microarray platforms across ten laboratories using identical RNA samples.