Cleaner

Cleaner refines assembly of informative, transcript-specific probe clusters for Affymetrix expression microarrays to improve data quality and reproducibility.

Key Features:

• R-system implementation: Implemented as an R-system software package for analysis of Affymetrix microarray probe data.
• Probe-level expression profile correlation: Uses probe-level expression profile correlation to identify uninformative or flawed probes.
• Probe elimination: Identifies and systematically eliminates problematic probes to enhance data reliability.
• Construction of improved probe sets: Constructs transcript-specific probe clusters and probe sets to increase accuracy and reproducibility.
• Accounting for probe dependence: Incorporates methods that account for dependencies between probes to reduce bias in data interpretation.
• Handling transcript-isoform variability: Implements strategies to mitigate variability arising from transcript-isoform mixtures.

Scientific Applications:

• Affymetrix microarray data improvement: Improves data quality and reproducibility of Affymetrix expression microarray experiments.
• Large-scale gene expression studies: Supports large-scale gene expression analyses requiring precise and reliable probe-level measurements.
• Cross-platform adaptation: Provides an approach that can be adapted to other gene expression profiling technologies beyond Affymetrix microarrays.

Methodology:

Probe-level expression profile correlation to identify and remove uninformative probes; construction of transcript-specific probe clusters/probe sets; methods to account for probe dependence; and strategies to mitigate transcript-isoform variability.