Optimising two-dye microarray designs for estimating associations with a quantitative trait.
We discuss how the samples should be arranged in two-dye microarray studies when the objective is to investigate associations between gene expression and quantitative traits measured on each sample. Because there is typically large between array variation, information about the association will come from the differences in traits and expression measurements between the two values hybridised to the two dyes on the same array. It is shown that within-slide correlation of trait values should be minimised. The arrangement of samples for which this occurs will depend on the trait values in question, and is a computationally demanding problem. An alternative is to minimise the rank correlation. We discuss this and related issues for different combinations of numbers of samples and arrays. Data analysis, including estimation of the variance components, is also described.
Horgan
G W
GW
Biomathematics & Statistics Scotland, Rowett Institute, Aberdeen AB21 9SB, UK. g.horgan@bioss.ac.uk
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004867:Equipment Design / Q000379:methods; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000295:instrumentation / Q000379:methods*; D036641:Microscopy, Fluorescence, Multiphoton / Q000295:instrumentation / Q000379:methods; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D011786:Quality Control; D040641:Quantitative Trait Loci / Q000235:genetics*; D013048:Specimen Handling / Q000379:methods
D005456:Fluorescent Dyes