affyPLM

affyPLM performs probe-level model fitting and PLM-based quality assessment of Affymetrix GeneChip microarray data to support accurate gene expression analysis.

Key Features:

• Probe-Level Model Fitting: Implements probe-level models (PLMs) to analyze expression at the individual probe level.
• PLM-Based Quality Assessment: Provides metrics and diagnostic plots derived from PLM methodologies to identify unwanted variation.
• Corrupted Chip Identification: Supports classification methods and pseudo-images to detect corrupted or problematic chips.
• RNA Quality Assessment: Facilitates assessment of RNA quality from formalin-embedded biopsies, laser-micro dissected samples, and single cells.
• Diagnostic Plot Generation: Produces diagnostic plots and quality metrics for evaluating microarray experiment quality.
• Compiled-Code Performance: Utilizes compiled code for rapid processing of large Affymetrix GeneChip datasets.

Scientific Applications:

• Affymetrix GeneChip expression analysis: Enables detailed probe-level investigations to improve accuracy of gene expression measurements.
• Microarray quality control: Identifies array-level issues and unwanted variation to improve data reliability.
• Challenging-sample analysis: Assesses RNA quality and array performance for formalin-embedded biopsies, laser-micro dissected samples, and single cells.
• Large-scale studies: Supports processing and quality assessment in projects with large volumes of microarray data.

Methodology:

Fits probe-level models (PLMs), applies PLM-based quality assessment using metrics and diagnostic plots, detects corrupted chips via classification methods and pseudo-images, and uses compiled code for rapid processing of Affymetrix GeneChip data.