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Comparison of the latest commercial short and long oligonucleotide microarray technologies
BACKGROUND: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™, GE Healthcare CodeLink™ and Agilent Technologies). The design of the comparison...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473202/ https://www.ncbi.nlm.nih.gov/pubmed/16539734 http://dx.doi.org/10.1186/1471-2164-7-51 |
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author | de Reyniès, Aurélien Geromin, Daniela Cayuela, Jean-Michel Petel, Fabien Dessen, Philippe Sigaux, François Rickman, David S |
author_facet | de Reyniès, Aurélien Geromin, Daniela Cayuela, Jean-Michel Petel, Fabien Dessen, Philippe Sigaux, François Rickman, David S |
author_sort | de Reyniès, Aurélien |
collection | PubMed |
description | BACKGROUND: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™, GE Healthcare CodeLink™ and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. RESULTS: All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms. CONCLUSION: We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels. |
format | Text |
id | pubmed-1473202 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-14732022006-06-03 Comparison of the latest commercial short and long oligonucleotide microarray technologies de Reyniès, Aurélien Geromin, Daniela Cayuela, Jean-Michel Petel, Fabien Dessen, Philippe Sigaux, François Rickman, David S BMC Genomics Research Article BACKGROUND: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™, GE Healthcare CodeLink™ and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. RESULTS: All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms. CONCLUSION: We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels. BioMed Central 2006-03-15 /pmc/articles/PMC1473202/ /pubmed/16539734 http://dx.doi.org/10.1186/1471-2164-7-51 Text en Copyright © 2006 de Reyniès et al; licensee BioMed Central Ltd. |
spellingShingle | Research Article de Reyniès, Aurélien Geromin, Daniela Cayuela, Jean-Michel Petel, Fabien Dessen, Philippe Sigaux, François Rickman, David S Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title | Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title_full | Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title_fullStr | Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title_full_unstemmed | Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title_short | Comparison of the latest commercial short and long oligonucleotide microarray technologies |
title_sort | comparison of the latest commercial short and long oligonucleotide microarray technologies |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473202/ https://www.ncbi.nlm.nih.gov/pubmed/16539734 http://dx.doi.org/10.1186/1471-2164-7-51 |
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