MBR

MBR removes blob-like image defects from Affymetrix oligonucleotide microarray .CEL files to improve probe-level sensitivity and reduce false discovery rate in downstream analyses.

Key Features:

• Visualization and detection: Rapid visualization and identification of blob-like defects of varying sizes and shapes within microarray images.
• Defect removal from .CEL files: Detection and removal of affected probes directly from Affymetrix .CEL files.
• Improved data quality: Removal of probes affected by blobs increases sensitivity and reduces false discovery rate in subsequent analyses.

Scientific Applications:

• Affymetrix ENCODE tiling arrays and high-density platforms: Applied to Affymetrix ENCODE tiling arrays and similar high-density microarray experiments where blob defects can obscure true signals.
• Spike-in target prediction assessment: Improves accuracy of spike-in target prediction used to evaluate array performance.

Methodology:

Detects and visualizes blob-like defects in microarray images and removes the corresponding probes from Affymetrix .CEL files; removal mitigates sensitivity loss and elevated FDR observed with Affymetrix tiling array software (TAS) and model-based analysis of tiling arrays (MAT).