Quality Control and Low-Level Statistical Analysis of Illumina BeadArray
The Illumina BeadArrayTM platform is a novel microarray technology based on randomly assembled arrays of beads. Each bead on the array carries copies of a single gene-specific probe with, on average, about 30 replicates of each bead type on an array. Given the encouraging results regarding the repr...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Instituto Nacional de Estatística | Statistics Portugal
2006-03-01
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| Series: | Revstat Statistical Journal |
| Subjects: | |
| Online Access: | https://revstat.ine.pt/index.php/REVSTAT/article/view/24 |
| _version_ | 1828354800421437440 |
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| author | Mark J. Dunning Natalie P. Thorne Isabelle Camilier Michael L. Smith Simon Tavaré |
| author_facet | Mark J. Dunning Natalie P. Thorne Isabelle Camilier Michael L. Smith Simon Tavaré |
| author_sort | Mark J. Dunning |
| collection | DOAJ |
| description |
The Illumina BeadArrayTM platform is a novel microarray technology based on randomly assembled arrays of beads. Each bead on the array carries copies of a single gene-specific probe with, on average, about 30 replicates of each bead type on an array. Given the encouraging results regarding the reproducibility of BeadArrayTM data and high profile studies already being carried out using the BeadArrayTM technology, there is likely to be an increase in the volume of BeadArrayTM data available. A major advantage of BeadArrayTM technology is the high degree of replication of beads of a given type. However, current analysis methods give summarised information for each bead type as output rather than information for each individual bead on the array. The beadarray R package is able to recreate individual bead information for arrays using raw images as input. Here, we use a particular experiment to illustrate the image processing steps used by Illumina and corresponding methods available in beadarray. Our investigations into BeadArrayTM data have demonstrated a high degree of reproducibility both within and between arrays. However, we identified some aspects of the low-level analysis that could be improved.
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| first_indexed | 2024-04-14T02:31:52Z |
| format | Article |
| id | doaj.art-2c27ef06c58341fa969648faae0bb184 |
| institution | Directory Open Access Journal |
| issn | 1645-6726 2183-0371 |
| language | English |
| last_indexed | 2024-04-14T02:31:52Z |
| publishDate | 2006-03-01 |
| publisher | Instituto Nacional de Estatística | Statistics Portugal |
| record_format | Article |
| series | Revstat Statistical Journal |
| spelling | doaj.art-2c27ef06c58341fa969648faae0bb1842022-12-22T02:17:39ZengInstituto Nacional de Estatística | Statistics PortugalRevstat Statistical Journal1645-67262183-03712006-03-014110.57805/revstat.v4i1.24Quality Control and Low-Level Statistical Analysis of Illumina BeadArrayMark J. Dunning 0Natalie P. Thorne 1Isabelle Camilier 2Michael L. Smith 3Simon Tavaré 4University of CambridgeUniversity of CambridgeEcole PolytechniqueUniversity of CambridgeUniversity of Cambridge The Illumina BeadArrayTM platform is a novel microarray technology based on randomly assembled arrays of beads. Each bead on the array carries copies of a single gene-specific probe with, on average, about 30 replicates of each bead type on an array. Given the encouraging results regarding the reproducibility of BeadArrayTM data and high profile studies already being carried out using the BeadArrayTM technology, there is likely to be an increase in the volume of BeadArrayTM data available. A major advantage of BeadArrayTM technology is the high degree of replication of beads of a given type. However, current analysis methods give summarised information for each bead type as output rather than information for each individual bead on the array. The beadarray R package is able to recreate individual bead information for arrays using raw images as input. Here, we use a particular experiment to illustrate the image processing steps used by Illumina and corresponding methods available in beadarray. Our investigations into BeadArrayTM data have demonstrated a high degree of reproducibility both within and between arrays. However, we identified some aspects of the low-level analysis that could be improved. https://revstat.ine.pt/index.php/REVSTAT/article/view/24IlluminaBeadArraybeadarrayBioconductormicroarray |
| spellingShingle | Mark J. Dunning Natalie P. Thorne Isabelle Camilier Michael L. Smith Simon Tavaré Quality Control and Low-Level Statistical Analysis of Illumina BeadArray Revstat Statistical Journal Illumina BeadArray beadarray Bioconductor microarray |
| title | Quality Control and Low-Level Statistical Analysis of Illumina BeadArray |
| title_full | Quality Control and Low-Level Statistical Analysis of Illumina BeadArray |
| title_fullStr | Quality Control and Low-Level Statistical Analysis of Illumina BeadArray |
| title_full_unstemmed | Quality Control and Low-Level Statistical Analysis of Illumina BeadArray |
| title_short | Quality Control and Low-Level Statistical Analysis of Illumina BeadArray |
| title_sort | quality control and low level statistical analysis of illumina beadarray |
| topic | Illumina BeadArray beadarray Bioconductor microarray |
| url | https://revstat.ine.pt/index.php/REVSTAT/article/view/24 |
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