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Statistical methodology for the analysis of dye-switch microarray experiments
BACKGROUND: In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurem...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2277403/ https://www.ncbi.nlm.nih.gov/pubmed/18271965 http://dx.doi.org/10.1186/1471-2105-9-98 |
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author | Mary-Huard, Tristan Aubert, Julie Mansouri-Attia, Nadera Sandra, Olivier Daudin, Jean-Jacques |
author_facet | Mary-Huard, Tristan Aubert, Julie Mansouri-Attia, Nadera Sandra, Olivier Daudin, Jean-Jacques |
author_sort | Mary-Huard, Tristan |
collection | PubMed |
description | BACKGROUND: In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurements that must be taken into account in the statistical analysis. RESULTS: We present two original statistical procedures for the statistical analysis of individually balanced designs. These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data. CONCLUSION: The UP procedure we propose as an alternative to usual mixed model procedures is more efficient and significantly faster to compute. This result provides some useful guidelines for the analysis of complex designs. |
format | Text |
id | pubmed-2277403 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-22774032008-04-01 Statistical methodology for the analysis of dye-switch microarray experiments Mary-Huard, Tristan Aubert, Julie Mansouri-Attia, Nadera Sandra, Olivier Daudin, Jean-Jacques BMC Bioinformatics Methodology Article BACKGROUND: In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurements that must be taken into account in the statistical analysis. RESULTS: We present two original statistical procedures for the statistical analysis of individually balanced designs. These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data. CONCLUSION: The UP procedure we propose as an alternative to usual mixed model procedures is more efficient and significantly faster to compute. This result provides some useful guidelines for the analysis of complex designs. BioMed Central 2008-02-13 /pmc/articles/PMC2277403/ /pubmed/18271965 http://dx.doi.org/10.1186/1471-2105-9-98 Text en Copyright © 2008 Mary-Huard et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Mary-Huard, Tristan Aubert, Julie Mansouri-Attia, Nadera Sandra, Olivier Daudin, Jean-Jacques Statistical methodology for the analysis of dye-switch microarray experiments |
title | Statistical methodology for the analysis of dye-switch microarray experiments |
title_full | Statistical methodology for the analysis of dye-switch microarray experiments |
title_fullStr | Statistical methodology for the analysis of dye-switch microarray experiments |
title_full_unstemmed | Statistical methodology for the analysis of dye-switch microarray experiments |
title_short | Statistical methodology for the analysis of dye-switch microarray experiments |
title_sort | statistical methodology for the analysis of dye-switch microarray experiments |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2277403/ https://www.ncbi.nlm.nih.gov/pubmed/18271965 http://dx.doi.org/10.1186/1471-2105-9-98 |
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