Methods for analysing raw Illumina BeadArray data
Illumina provide a novel technology for measuring transcript abundance (for example) by use of randomly assembled arrays of beads, each of which has a
probe for a specific transcript. The random nature of the arrays (for example, each bead type occurs a random number of times in random locations on the array) leads to a number of novel statistical problems that we have addressed.
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Images of illumina artefacts and the regions masked by BASH
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Illumina provides its BeadStudio software that reports, among other things, the average intensity of each bead-type on an array and measures of the quality of that bead-type. Illumina’s BeadScan software can now be asked to report full bead-level data, thus opening up their data to analysis by other techniques, and We have devoted considerable effort to the development of the open source beadarray software for the extraction and analysis of raw bead-level data. The beadarray package has proved popular, being downloaded 6618 times in 2008
Using beadarray, we have investigated the benefits of using bead level data over using Bead-Studio's summarized data, and have found that careful treatment of the data can increase the power of analyses. The bead-level information is also required to satisfactorily remove spatial artefacts, for which we have the BASH function, and to handle two-colour Illumina platforms appropriately.
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| Selected publications of ours in this area |
- Dunning MJ, Smith ML, Ritchie ME, Tavaré S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007 Aug 15;23(16):2183-4. Epub 2007 Jun 22 [pubmed]
- Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME. Statistical issues in the analysis of Illumina data. BMC Bioinformatics 2008 9:85 [publisher online]
- Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. BASH: A tool for managing BeadArray spatial artefacts Bioinformatics 2008
Oct 25;24(24):2921-2 [publisher online]
- Lynch AG, Dunning MJ, Iddawela M, Barbosa-Morais NL, Ritchie ME. Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms
Statistical Methods in Medical Research in press.
- Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S, Lynch AG. Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Research Notes, 2008 1:18 [publisher online]
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