ArrayAnalysis

ArrayAnalysis performs quality control, pre-processing, statistical analysis, and pathway analysis for transcriptomic datasets from Affymetrix microarrays, Illumina whole-genome expression bead arrays, and RNA-seq.

Key Features:

• Quality Control and Pre-processing: Incorporates QC algorithms to generate quality control plots and produce normalized datasets for microarray and RNA-seq data.
• Platform Support: Supports Affymetrix microarrays and Illumina whole-genome expression bead arrays, including import of GenomeStudio output for Illumina data.
• Integration with R/Bioconductor: Extends and harmonizes functionalities from R and Bioconductor packages to enable Affymetrix analyses and downstream statistical and pathway workflows.
• Statistical and Pathway Analysis: Provides statistical evaluations including identification of differentially expressed genes and pathway analysis capabilities.
• Modular Architecture: Modular open-source architecture that permits addition of modules to support additional data types or extend existing workflows.
• Interoperability: Enables export of processed data for downstream analyses with third-party tools.

Scientific Applications:

• Transcriptomic Quality Assessment: Quality control and normalization of microarray and RNA-seq datasets to ensure data integrity for downstream analyses.
• Differential Expression Analysis: Identification of differentially expressed genes from Affymetrix, Illumina bead arrays, and RNA-seq experiments.
• Pathway and Functional Interpretation: Pathway exploration and enrichment analyses to interpret gene expression changes.
• Cross-platform Processing and Data Reuse: Processing and harmonization of Affymetrix and Illumina bead array data to facilitate data reuse and comparative analyses.

Methodology:

Performs quality control, generates QC plots, performs normalization to produce normalized datasets, imports GenomeStudio output for Illumina bead arrays, conducts statistical evaluations to identify differentially expressed genes, and runs pathway analyses using integrated R/Bioconductor functionality.