affycomp

affycomp evaluates expression measures derived from Affymetrix Oligonucleotide Arrays by comparing summarization methods against dilution and spike-in benchmark datasets to assess statistical and biological performance.

Key Features:

• Probe-level visualization: Generates plots to visualize and compare probe-level summary statistics across summarization methods.
• Benchmark datasets: Uses dilution studies and spike-in experiments as gold-standard datasets for performance assessment.
• Summary statistics and plots: Produces summary statistics and graphical summaries to characterize statistical properties of expression measures.
• Biological relevance assessment: Emphasizes features that align expression measures with biological questions and expected outcomes.

Scientific Applications:

• Gene expression profiling: Compares summarization methods to select measures that yield biologically meaningful expression profiles from Affymetrix arrays.
• Differential expression analysis: Informs selection of expression measures to improve accuracy of differential expression detection.
• Validation studies: Benchmarks new or existing summarization methods against known dilution and spike-in outcomes.

Methodology:

Generates probe-level plots for visual comparison; uses dilution and spike-in benchmark datasets to evaluate statistical properties of summarization methods; allows tailoring the analysis to focus on specific probe-level features.