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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...

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Autores principales: Mary-Huard, Tristan, Aubert, Julie, Mansouri-Attia, Nadera, Sandra, Olivier, Daudin, Jean-Jacques
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
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.
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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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