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...
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| Veröffentlicht in: | Journal of biotechnology 2005-07, Vol.118 (1), p.1-8 |
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| container_title | Journal of biotechnology |
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| creator | Horgan, G.W. |
| description | 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. |
| doi_str_mv | 10.1016/j.jbiotec.2005.02.016 |
| format | Article |
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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. 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Psychology</topic><topic>Gene Expression Profiling - instrumentation</topic><topic>Gene Expression Profiling - methods</topic><topic>Genetic Variation - genetics</topic><topic>In Situ Hybridization, Fluorescence - instrumentation</topic><topic>In Situ Hybridization, Fluorescence - methods</topic><topic>Loop</topic><topic>Microarray</topic><topic>Microscopy, Fluorescence, Multiphoton - instrumentation</topic><topic>Microscopy, Fluorescence, Multiphoton - methods</topic><topic>Models, Genetic</topic><topic>Models, Statistical</topic><topic>Oligonucleotide Array Sequence Analysis - instrumentation</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Quality Control</topic><topic>Quantitative trait</topic><topic>Quantitative Trait Loci - genetics</topic><topic>Specimen Handling - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Horgan, G.W.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Horgan, G.W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Optimising two-dye microarray designs for estimating associations with a quantitative trait</atitle><jtitle>Journal of biotechnology</jtitle><addtitle>J Biotechnol</addtitle><date>2005-07-21</date><risdate>2005</risdate><volume>118</volume><issue>1</issue><spage>1</spage><epage>8</epage><pages>1-8</pages><issn>0168-1656</issn><eissn>1873-4863</eissn><coden>JBITD4</coden><abstract>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. 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| ispartof | Journal of biotechnology, 2005-07, Vol.118 (1), p.1-8 |
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| language | eng |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Algorithms Biological and medical sciences Biotechnology Chromosome Mapping - methods Equipment Design - methods Fluorescent Dyes Fundamental and applied biological sciences. Psychology Gene Expression Profiling - instrumentation Gene Expression Profiling - methods Genetic Variation - genetics In Situ Hybridization, Fluorescence - instrumentation In Situ Hybridization, Fluorescence - methods Loop Microarray Microscopy, Fluorescence, Multiphoton - instrumentation Microscopy, Fluorescence, Multiphoton - methods Models, Genetic Models, Statistical Oligonucleotide Array Sequence Analysis - instrumentation Oligonucleotide Array Sequence Analysis - methods Quality Control Quantitative trait Quantitative Trait Loci - genetics Specimen Handling - methods |
| title | Optimising two-dye microarray designs for estimating associations with a quantitative trait |
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