Optimal factorial designs for cDNA microarray experiments
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1,122 citations
"Optimal factorial designs for cDNA ..." refers background or methods in this paper
...We refer to Kerr and Churchill (2001b), Yang and Speed (2002) and Churchill (2002) for very informative further discussion on the design issues....
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..., a design where every treatment combination appears an even number of times) allows a dye-color assignment that ensures orthogonality to η [Kerr and Churchill (2001a)]....
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...While Kerr and Churchill (2001a, 2001b) and Churchill (2002) concentrated on varietal designs, Yang and Speed (2002) discussed factorial designs in some detail....
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...…work on varietal designs for microarrays includes those due to Dobbin and Simon (2002), Kerr (2003), Rosa, Steibel and Tempelman (2005), Wit, Nobile and Khanin (2005) and Altman and Hua (2006), although some of these authors, as also Churchill (2002), briefly touched upon factorial designs as well....
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...Then, for the purpose of estimating the θs, the means of the r log intensity ratios arising from the slides play the role of the individual ratios considered so far, but an attempt to estimate σ2 on the basis of the within slide variation can be vitiated by unknown correlation among the ratios arising from the same slide [Yang and Speed (2002) and Churchill (2002)]....
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824 citations
"Optimal factorial designs for cDNA ..." refers background or methods or result in this paper
...We consider the baseline parametrization [cf. Yang and Speed (2002); GS] according to which the main effects of F1 and F2 are given respectively by θ10 = τ10 − τ00 and θ01 = τ01 − τ00,(1) while the interaction effect F1F2 is given by θ11 = τ11 − τ10 − τ01 + τ00....
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...We refer to Kerr and Churchill (2001b), Yang and Speed (2002) and Churchill (2002) for very informative further discussion on the design issues....
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...While Kerr and Churchill (2001a, 2001b) and Churchill (2002) concentrated on varietal designs, Yang and Speed (2002) discussed factorial designs in some detail....
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...Turning to factorial designs for microarrays under the baseline parametrization, which is the main thrust of this paper, two key references are Yang and Speed (2002) and Glonek and Solomon (2004), (hereafter abbreviated GS)....
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...The following results confirm this and, hence, vindicate the proposal of Yang and Speed (2002) about dye-swapping....
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701 citations
614 citations
"Optimal factorial designs for cDNA ..." refers background or methods or result in this paper
...We refer to Kerr and Churchill (2001b), Yang and Speed (2002) and Churchill (2002) for very informative further discussion on the design issues....
[...]
...While Kerr and Churchill (2001a, 2001b) and Churchill (2002) concentrated on varietal designs, Yang and Speed (2002) discussed factorial designs in some detail....
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...In a pioneering paper Kerr and Churchill (2001a) discussed the design issues in microarrays and investigated optimal varietal designs that estimate the pairwise contrasts of treatment effects for fixed genes with minimum average variance....
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...For this reduced model, it is known that any even design (i.e., a design where every treatment combination appears an even number of times) allows a dye-color assignment that ensures orthogonality to η [Kerr and Churchill (2001a)]....
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...The above experimental setup is structurally similar to classical paired comparison experiments; see Kerr and Churchill (2001a)....
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486 citations
"Optimal factorial designs for cDNA ..." refers background or result in this paper
...This reinforces the findings in Kerr (2003) in a simpler setting and suggests that, in addition to making the log intensity ratios from different slides uncorrelated, use of only biological replicates can be advantageous from the perspective of design efficiency as well; see also Kendziorski et al. (2005) and the references therein for insightful practical results in a similar context. The point just noted makes sense if the cost of biological replication is negligible compared to the cost of the assay per slide, as has been tacitly supposed in this paper. While Bueno Filho, Gilmour and Rosa (2006) mention that the number of slides is typically the most important limiting factor in microarray experiments, a more detailed discussion in this regard is available in Kerr (2003), who also dwelt on the situation where this is not the case. If the cost of biological replication is a real issue, then the design problem becomes much more complex. Instead of fixing the number of slides, as done here, one should then proceed in the spirit of Kerr (2003) to formulate the problem in terms of a cost function that incorporates the cost of the assays (slides), as well as the cost of biological replication....
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...This reinforces the findings in Kerr (2003) in a simpler setting and suggests that, in addition to making the log intensity ratios from different slides uncorrelated, use of only biological replicates can be advantageous from the perspective of design efficiency as well; see also Kendziorski et al. (2005) and the references therein for insightful practical results in a similar context....
[...]
...This reinforces the findings in Kerr (2003) in a simpler setting and suggests that, in addition to making the log intensity ratios from different slides uncorrelated, use of only biological replicates can be advantageous from the perspective of design efficiency as well; see also Kendziorski et al. (2005) and the references therein for insightful practical results in a similar context. The point just noted makes sense if the cost of biological replication is negligible compared to the cost of the assay per slide, as has been tacitly supposed in this paper. While Bueno Filho, Gilmour and Rosa (2006) mention that the number of slides is typically the most important limiting factor in microarray experiments, a more detailed discussion in this regard is available in Kerr (2003), who also dwelt on the situation where this is not the case....
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...Kerr (2003) and Altman and Hua (2006), among others] with common value say, γ2, then the log intensity ratios arising from different slides are homoscedastic with common variance σ2 = 2γ2 + δ2....
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...This reinforces the findings in Kerr (2003) in a simpler setting and suggests that, in addition to making the log intensity ratios from different slides uncorrelated, use of only biological replicates can be advantageous from the perspective of design efficiency as well; see also Kendziorski et al....
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