AgiMicroRna

AgiMicroRna processes and analyzes microRNA data from Agilent microarray platforms for pre-processing and differential expression analysis.

Key Features:

• RMA pre-processing: Pre-processing using the robust multiarray average (RMA) algorithm with a linear model that accounts for probe affinity effects.
• Alternative signal input: Option to use signals generated by Agilent's image analysis software instead of RMA-processed signals.
• Normalization and quality assessment: Graphical utilities for data quality assessment and normalization of microRNA signals for downstream analyses.
• Differential expression analysis: Differential expression testing implemented with limma linear models to compare experimental conditions.
• miRBase linkage: Significant microRNAs can be linked to miRBase for sequence and annotation information.
• Implementation and integration: Implemented in R and integrated into the Bioconductor project.

Scientific Applications:

• MicroRNA expression profiling: Identification of microRNAs involved in various cellular processes using Agilent microarray data.
• Differential expression studies: Detection of differentially expressed microRNAs between experimental conditions for studies of health and disease.
• MicroRNA regulation and function analysis: Support for analyses aimed at understanding microRNA regulation and function through processed microarray data.

Methodology:

Pre-processing uses RMA (robust multiarray average) with a probe-affinity linear model or optional Agilent image-analysis signals, followed by normalization and graphical QC, differential expression via limma linear models, and linking of results to miRBase; implemented in R within Bioconductor.