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    Analyzing Multiple-Probe Microarray: Estimation and Application of Gene Expression Indexes

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    Type
    Article
    Authors
    Maadooliat, Mehdi
    Huang, Jianhua Z.
    Hu, Jianhua
    KAUST Grant Number
    KUS-CI-016-04
    Date
    2012-07-26
    Online Publication Date
    2012-07-26
    Print Publication Date
    2012-09
    Permanent link to this record
    http://hdl.handle.net/10754/597571
    
    Metadata
    Show full item record
    Abstract
    Gene expression index estimation is an essential step in analyzing multiple probe microarray data. Various modeling methods have been proposed in this area. Amidst all, a popular method proposed in Li and Wong (2001) is based on a multiplicative model, which is similar to the additive model discussed in Irizarry et al. (2003a) at the logarithm scale. Along this line, Hu et al. (2006) proposed data transformation to improve expression index estimation based on an ad hoc entropy criteria and naive grid search approach. In this work, we re-examined this problem using a new profile likelihood-based transformation estimation approach that is more statistically elegant and computationally efficient. We demonstrate the applicability of the proposed method using a benchmark Affymetrix U95A spiked-in experiment. Moreover, We introduced a new multivariate expression index and used the empirical study to shows its promise in terms of improving model fitting and power of detecting differential expression over the commonly used univariate expression index. As the other important content of the work, we discussed two generally encountered practical issues in application of gene expression index: normalization and summary statistic used for detecting differential expression. Our empirical study shows somewhat different findings from the MAQC project (MAQC, 2006).
    Citation
    Maadooliat M, Huang JZ, Hu J (2012) Analyzing Multiple-Probe Microarray: Estimation and Application of Gene Expression Indexes. Biometrics 68: 784–792. Available: http://dx.doi.org/10.1111/j.1541-0420.2012.01727.x.
    Sponsors
    We would like to thank an AE and a referee for their constructive comments. Mehdi Maadooliat and Jianhua Hu were supported by the National Science Foundation Grant DMS-0706818, National Institutes of Health Grants R01GM080503-01A1, R21CA129671, Cancer Center Support Grant P30 CA016672, and National Cancer Institute CA97007. Jianhua Z. Huang was supported by NSF (DMS-0606580, DMS-0907170), NCI (CA57030), and King Abdullah University of Science and Technology (KUS-CI-016-04). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.
    Publisher
    Wiley
    Journal
    Biometrics
    DOI
    10.1111/j.1541-0420.2012.01727.x
    PubMed ID
    22834966
    PubMed Central ID
    PMC3989902
    ae974a485f413a2113503eed53cd6c53
    10.1111/j.1541-0420.2012.01727.x
    Scopus Count
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