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BASH: a tool for managing BeadArray spatial artefacts.

J M Cairns¹, M J Dunning, M E Ritchie

¹Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB20RE, UK.

Bioinformatics (Oxford, England)

|October 28, 2008

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Illumina BeadArrays can detect spatial artifacts better than other microarray technologies. We present BASH, a new tool designed to identify and remove these artifacts using bead-level data for improved analysis.

Area of Science:

Genomics
Bioinformatics
Microarray Technology

Background:

Illumina BeadArrays offer enhanced capabilities for detecting spatial artifacts due to their design.
Existing tools for artifact detection and exclusion are not optimized for Illumina technology.
The beadarray Bioconductor package (version 1.10 onwards) is available for use.

Purpose of the Study:

To introduce BASH, a novel bioinformatics tool for identifying and excluding spatial artifacts in Illumina BeadArray data.
To leverage the unique characteristics of Illumina technology for more effective artifact analysis.

Main Methods:

BASH adopts concepts from the Harshlight tool but is specifically implemented for Illumina BeadArrays.
The tool utilizes bead-level data for comprehensive spatial artifact detection.

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Analysis focuses on identifying and excluding various types of spatial artifacts.

Main Results:

BASH enables the identification of spatial artifacts in Illumina BeadArray data.
The tool facilitates the exclusion of detected artifacts from downstream analyses.
Demonstrates robustness to artifact exclusion.

Conclusions:

BASH provides a much-needed tool for spatial artifact detection and exclusion in Illumina BeadArray experiments.
The tool enhances the reliability of microarray data analysis by addressing technology-specific challenges.
Improved data quality through artifact removal leads to more accurate biological interpretations.