國家衛生研究院 NHRI:Item 3990099045/1798
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/1798


    Title: Evaluation of experimental designs for two-color cDNA microarrays
    Authors: Yang, CW;Hsiao, CF;Chou, CK
    Contributors: Division of Biostatistics and Bioinformatics;Division of Molecular and Genomic Medicine
    Abstract: The major goal of two-color cDNA microarray experiments is to measure the relative gene expression level (i.e., relative amount of mRNA) of each gene between samples in studies of gene expression. More specifically, given an N-sample experiment, we need all N(N-1)/2 relative expression levels of all sample pairs of each gene for identification of the differentially expressed genes and for clustering of gene expression patterns. However, the intensities observed from two-color cDNA microarray experiments do not simply represent the relative gene expression level. They are composed of signal (gene expression level), noise, and other factors. In discussions on the experimental design of two-color cDNA microarray experiments, little attention has been given to the fact that different combinations of test and control samples will produce microarray intensities data with varying intrinsic composition of factors. As a consequence, not all experimental designs for two-color cDNA microarray experiments are able to provide all possible relative gene expression levels. This phenomenon has never been addressed. To obtain all possible relative gene expression levels, a novel method for two-color cDNA microarray experimental design evaluation is necessary that will allow the making of an accurate choice. In this study, we propose a model-based approach to illustrate how the factor composition of microarray intensities changed with different experimental designs in two-color cDNA microarray experiments. By analyzing 12 experimental designs (including 5 general forms), we demonstrate that not all experimental designs are able to provide all possible relative gene expression levels due to the differences in factor composition. Our results indicate that whether an experimental design can provide all possible relative expression levels of all sample pairs for each gene should be the first criterion to be considered in an evaluation of experimental designs for two-color cDNA microarray experiments.
    Keywords: Biochemical Research Methods;Biotechnology & Applied Microbiology;Computer Science, Interdisciplinary Applications;Mathematical & Computational Biology;Statistics & Probability
    Date: 2005-11
    Relation: Journal of Computational Biology. 2005 Nov;12(9):1202-1220.
    Link to: http://dx.doi.org/10.1089/cmb.2005.12.1202
    JIF/Ranking 2023: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=NHRI&SrcApp=NHRI_IR&KeyISSN=1066-5277&DestApp=IC2JCR
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000233857000005
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=28744435112
    Appears in Collections:[Chin-Fu Hsiao] Periodical Articles
    [Others] Periodical Articles

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