Limits...
Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays.

Townsend JP - BMC Genomics (2003)

Bottom Line: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu

ABSTRACT

Background: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.

Results: A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.

Conclusions: In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

Show MeSH

Related in: MedlinePlus

A depiction of common strategies for microarray experimental design. A) Each sample is tested against a single, common standard. B) A pooled sample, made up of equal parts of a number of samples, is used for comparison to the samples of interest. C) Each strain is compared head-to-head with other strains in a circular fashion, or, D) with added cross-comparisons, a multiple-pairwise fashion. This last example is a classical balanced block design, with dye swaps.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC239860&req=5

Figure 1: A depiction of common strategies for microarray experimental design. A) Each sample is tested against a single, common standard. B) A pooled sample, made up of equal parts of a number of samples, is used for comparison to the samples of interest. C) Each strain is compared head-to-head with other strains in a circular fashion, or, D) with added cross-comparisons, a multiple-pairwise fashion. This last example is a classical balanced block design, with dye swaps.

Mentions: In complex designs, the pairwise nature of spotted DNA microarray hybridizations permits multiple comparison structures. Most multiple-comparison spotted DNA microarray studies to date can be characterized as one of three types of experimental design. In the "reference sample" strategy depicted in Figure 1A, each sample is tested against a single, common standard (e.g. [8-10]). The advantage of this approach is the simplicity with which it is implemented. However, it has three disadvantages. First, because it pairs the reference strain with every other strain, it provides more information on the expression levels of the reference strain than on any other. Unless the reference strain is of primary interest, the focus in the experimental design upon its expression level is wasteful. Second, all comparisons of other strains in the design to each other are made in a purely transitive fashion, which is less precise and subject to greater experimental noise than direct comparison [11,12]. Third, use of a single reference may lead to difficulty in estimating gene expression levels for genes that are at low expression level in the reference strain compared to other strains. The expression levels estimated for these genes will be particularly inaccurate because experimental error in the measurement of the sample with lower gene expression will lead to enormous variance in the ratios observed.


Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays.

Townsend JP - BMC Genomics (2003)

A depiction of common strategies for microarray experimental design. A) Each sample is tested against a single, common standard. B) A pooled sample, made up of equal parts of a number of samples, is used for comparison to the samples of interest. C) Each strain is compared head-to-head with other strains in a circular fashion, or, D) with added cross-comparisons, a multiple-pairwise fashion. This last example is a classical balanced block design, with dye swaps.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC239860&req=5

Figure 1: A depiction of common strategies for microarray experimental design. A) Each sample is tested against a single, common standard. B) A pooled sample, made up of equal parts of a number of samples, is used for comparison to the samples of interest. C) Each strain is compared head-to-head with other strains in a circular fashion, or, D) with added cross-comparisons, a multiple-pairwise fashion. This last example is a classical balanced block design, with dye swaps.
Mentions: In complex designs, the pairwise nature of spotted DNA microarray hybridizations permits multiple comparison structures. Most multiple-comparison spotted DNA microarray studies to date can be characterized as one of three types of experimental design. In the "reference sample" strategy depicted in Figure 1A, each sample is tested against a single, common standard (e.g. [8-10]). The advantage of this approach is the simplicity with which it is implemented. However, it has three disadvantages. First, because it pairs the reference strain with every other strain, it provides more information on the expression levels of the reference strain than on any other. Unless the reference strain is of primary interest, the focus in the experimental design upon its expression level is wasteful. Second, all comparisons of other strains in the design to each other are made in a purely transitive fashion, which is less precise and subject to greater experimental noise than direct comparison [11,12]. Third, use of a single reference may lead to difficulty in estimating gene expression levels for genes that are at low expression level in the reference strain compared to other strains. The expression levels estimated for these genes will be particularly inaccurate because experimental error in the measurement of the sample with lower gene expression will lead to enormous variance in the ratios observed.

Bottom Line: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu

ABSTRACT

Background: Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.

Results: A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.

Conclusions: In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.

Show MeSH
Related in: MedlinePlus