Limits...
Statistical methodology for the analysis of dye-switch microarray experiments.

Mary-Huard T, Aubert J, Mansouri-Attia N, Sandra O, Daudin JJ - BMC Bioinformatics (2008)

Bottom Line: These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR AgroParisTech/INRA 518, 16, rue Claude Bernard 75231 Paris CEDEX 05, France. maryhuar@agroparistech.fr

ABSTRACT

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.

Show MeSH
The Teleofish experiment design.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2277403&req=5

Figure 4: The Teleofish experiment design.

Mentions: An important application of the methodology proposed in the previous section is the analysis of loop design experiments. Loop and interwoven loop designs were initially proposed in [2] to compare p treatments, where p is 3 or higher. Figure 4 displays a particular interwoven loop design where 3 different 2-by-2 loop comparisons of treatments are combined in a single experiment. The 3 loop comparisons are


Statistical methodology for the analysis of dye-switch microarray experiments.

Mary-Huard T, Aubert J, Mansouri-Attia N, Sandra O, Daudin JJ - BMC Bioinformatics (2008)

The Teleofish experiment design.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277403&req=5

Figure 4: The Teleofish experiment design.
Mentions: An important application of the methodology proposed in the previous section is the analysis of loop design experiments. Loop and interwoven loop designs were initially proposed in [2] to compare p treatments, where p is 3 or higher. Figure 4 displays a particular interwoven loop design where 3 different 2-by-2 loop comparisons of treatments are combined in a single experiment. The 3 loop comparisons are

Bottom Line: These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR AgroParisTech/INRA 518, 16, rue Claude Bernard 75231 Paris CEDEX 05, France. maryhuar@agroparistech.fr

ABSTRACT

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.

Show MeSH