oneChannelGUI

oneChannelGUI provides comprehensive analysis of single-channel microarray data using Bioconductor libraries, with emphasis on Affymetrix 3' expression (IVT) arrays and whole-transcript Gene/Exon 1.0 ST arrays.

Key Features:

• Bioconductor integration: Add-on package that extends affylmGUI and integrates existing Bioconductor libraries for microarray analysis.
• Single-channel array support: Supports Affymetrix 3' expression (IVT) arrays and whole-transcript Gene/Exon 1.0 ST arrays.
• Quality control: Implements rigorous quality assessment protocols for microarray data integrity.
• Normalization: Provides various normalization techniques to adjust for systematic biases.
• Filtering: Enables removal of low-quality or irrelevant probes/probesets to improve downstream analyses.
• Statistical validation: Includes robust statistical methods for assessing significance of results.
• Data mining: Facilitates extraction of meaningful patterns and insights from large datasets.
• miRNA/mRNA-seq support: Supports analysis workflows that include miRNA and mRNA-seq data.

Scientific Applications:

• Gene expression profiling: Generation and analysis of gene-level expression results from single-channel arrays.
• Exon-level analysis: Analysis of exon-level expression using whole-transcript Gene/Exon 1.0 ST arrays.
• miRNA and mRNA sequencing analysis: Integration of miRNA/mRNA-seq data analyses alongside microarray data.

Methodology:

Integration of existing Bioconductor tools by extending affylmGUI to provide end-to-end processing steps from quality control through normalization, filtering, statistical validation, and data mining.