MArray

MArray analyzes microarray datasets, providing a Matlab-based framework to process raw microarray output from QuantArray and GenePiX for quality evaluation, normalization, reproducibility assessment of single and paired experiments, and integration with NCBI UniGene.

Key Features:

• Data Input Flexibility: Accepts raw microarray output files from image analysis software such as QuantArray and GenePiX.
• Experimental Design Support: Supports analysis of both single and paired microarray experiments.
• Quality Evaluation: Provides functions for manual evaluation of measurement quality.
• Normalization Techniques: Implements simple normalization and intensity-dependent normalization methods.
• Reproducibility Assessment: Evaluates reproducibility for paired experiments using a simple statistical method, quality control ellipse, and significance analysis of microarrays.
• Gene Information Integration: Links results to NCBI UniGene for gene annotation and information retrieval.

Scientific Applications:

• Experimental Optimization: Optimization and selection of experimental procedures through quality control and reproducibility analysis.
• Two-state Comparisons: Analysis of two-state biological comparisons to detect differential expression between conditions.
• Single-dose Activation Studies: Investigation of single-dose activation to detect gene expression responses to a single treatment or stimulus.

Methodology:

Implemented in Matlab; accepts raw output from QuantArray and GenePiX; provides functions for manual measurement quality evaluation; applies simple and intensity-dependent normalization; assesses reproducibility using a simple statistical method, quality control ellipse, and significance analysis of microarrays; integrates NCBI UniGene for gene annotation.