AffyGCQC

AffyGCQC assesses quality of Affymetrix GeneChip oligonucleotide array data and detects outlier arrays to support reliable differential gene expression analysis.

Key Features:

• Graphical Representation of QC Metrics: Visualizes Affymetrix-recommended QC metrics for GeneChip oligonucleotide arrays.
• Extreme Studentized Deviate (ESD) Statistical Tests: Implements extreme studentized deviate (ESD) tests to identify outlier arrays within experimental sets.

Scientific Applications:

• Preprocessing Quality Control: Performs QC in preprocessing to exclude poor-quality arrays before downstream differential gene expression analysis.
• Outlier Detection: Detects technical artifacts and outlier arrays that can confound biological interpretation.
• Large-Scale Consistency Assessment: Assesses consistency across multiple arrays and experiments in large-scale studies.

Methodology:

Integrates Affymetrix-recommended QC metrics with extreme studentized deviate (ESD) statistical testing and produces graphical representations of QC metrics.