affylmGUI

affylmGUI performs preprocessing, quality control, and differential expression analysis of Affymetrix CEL microarray data using Bioconductor 'affy' preprocessing and 'limma' linear models with empirical Bayes.

Key Features:

• Integrated workflow: Processes Affymetrix CEL files through quality control, pre-processing, normalization, and downstream analysis.
• Quality control and pre-processing: Implements QC measures and offers normalization and transformation options for array data.
• Differential expression analysis: Uses linear models with empirical Bayes smoothing via the 'limma' package to identify differentially expressed genes.
• Bioconductor package integration: Combines the 'affy' package for preprocessing and normalization with 'limma' for statistical analysis.
• Exportable outputs: Generates analysis results as tables, figures, and HTML reports.

Scientific Applications:

• Cancer research: Identifying genes differentially expressed between cancerous and normal tissues using Affymetrix microarrays.
• Developmental biology: Studying gene expression changes across developmental stages or environmental conditions.
• Pharmacogenomics: Investigating gene expression patterns related to drug response variability.

Methodology:

Input CEL files undergo quality control and preprocessing with the 'affy' package for normalization and transformation, followed by differential expression analysis using 'limma' linear models with empirical Bayes smoothing to stabilize inference across genes.