spkTools

spkTools facilitates cross-platform comparison of microarray expression measures using spike-in experiments and statistical methods to assess platform performance.

Key Features:

• Spike-In Experiment Integration: Leverages spike-in experiments as controlled internal benchmarks for technology assessment and for comparing data analysis methodologies.
• Novel Statistical Solutions: Provides statistical techniques that enable meaningful comparisons of reported concentrations and expression measures across diverse microarray platforms.
• Bioconductor Implementation: Implemented as a Bioconductor package for integration into Bioconductor-based analysis workflows.
• Comprehensive Assessment Procedures: Includes a detailed procedure for conducting assessments based on spike-in experiments to evaluate platform performance.

Scientific Applications:

• Cross-Platform Microarray Comparison: Enables direct comparison of expression data generated on microarray platforms such as Affymetrix, Agilent, and Illumina.
• Platform and Method Evaluation: Supports evaluation of platform performance and comparison of data analysis methods for genomics studies using microarray data.

Methodology:

Conducts two spike-in experiments that serve as benchmarks for cross-platform comparison and applies the package's novel statistical methods to assess platform performance.