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  • Oxford University Press (OUP)  (6)
  • 2005-2009  (6)
  • 1
    Online Resource
    Online Resource
    Semiparametric Estimation in General Repeated Measures Problems
    Oxford University Press (OUP) ; 2006
    In:  Journal of the Royal Statistical Society Series B: Statistical Methodology Vol. 68, No. 1 ( 2006-02-01), p. 69-88
    Details
    In: Journal of the Royal Statistical Society Series B: Statistical Methodology, Oxford University Press (OUP), Vol. 68, No. 1 ( 2006-02-01), p. 69-88
    Abstract: The paper considers a wide class of semiparametric problems with a parametric part for some covariate effects and repeated evaluations of a nonparametric function. Special cases in our approach include marginal models for longitudinal or clustered data, conditional logistic regression for matched case–control studies, multivariate measurement error models, generalized linear mixed models with a semiparametric component, and many others. We propose profile kernel and backfitting estimation methods for these problems, derive their asymptotic distributions and show that in likelihood problems the methods are semiparametric efficient. Although generally not true, it transpires that with our methods profiling and backfitting are asymptotically equivalent. We also consider pseudolikelihood methods where some nuisance parameters are estimated from a different algorithm. The methods proposed are evaluated by using simulation studies and applied to the Kenya haemoglobin data.
    Type of Medium: Online Resource
    ISSN: 1369-7412 , 1467-9868
    URL: Article
    DOI: 10.1111/j.1467-9868.2005.00533.x
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2006
    detail.hit.zdb_id: 204795-0
    detail.hit.zdb_id: 1490719-7
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  • 2
    Online Resource
    Online Resource
    Genotypes and haplotypes of matrix metalloproteinase 1, 3 and 12 genes and the risk of lung cancer
    Oxford University Press (OUP) ; 2006
    In:  Carcinogenesis Vol. 27, No. 5 ( 2006-05-01), p. 1024-1029
    Details
    In: Carcinogenesis, Oxford University Press (OUP), Vol. 27, No. 5 ( 2006-05-01), p. 1024-1029
    Type of Medium: Online Resource
    ISSN: 1460-2180 , 0143-3334
    URL: Article
    DOI: 10.1093/carcin/bgi283
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2006
    detail.hit.zdb_id: 1474206-8
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  • 3
    Online Resource
    Online Resource
    Generalized Monotonic Functional Mixed Models with Application to Modelling Normal Tissue Complications
    Oxford University Press (OUP) ; 2008
    In:  Journal of the Royal Statistical Society Series C: Applied Statistics Vol. 57, No. 2 ( 2008-04-01), p. 149-163
    Details
    In: Journal of the Royal Statistical Society Series C: Applied Statistics, Oxford University Press (OUP), Vol. 57, No. 2 ( 2008-04-01), p. 149-163
    Abstract: Normal tissue complications are a common side effect of radiation therapy. They are the consequence of the dose of radiation that is received by the normal tissue surrounding the site of the tumour. Within a specified organ each voxel receives a certain dose of radiation, leading to a distribution of doses over the organ. It is often not known what aspect of the dose distribution drives the presence and severity of the complications. A summary measure of the dose distribution can be obtained by integrating a weighting function of dose (w(d)) over the density of dose. For biological reasons the weight function should be monotonic. We propose a generalized monotonic functional mixed model to study the dose effect on a clinical outcome by estimating this weight function non-parametrically by using splines and subject to the monotonicity constraint, while allowing for overdispersion and correlation of multiple obervations within the same subject. We illustrate our method with data from a head and neck cancer study in which the irradiation of the parotid gland results in loss of saliva flow.
    Type of Medium: Online Resource
    ISSN: 0035-9254 , 1467-9876
    URL: Article
    DOI: 10.1111/j.1467-9876.2007.00606.x
    RVK:
    SA 7810
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 204797-4
    detail.hit.zdb_id: 1482300-7
    detail.hit.zdb_id: 1476894-X
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  • 4
    Online Resource
    Online Resource
    Apoptosis gene polymorphisms, age, smoking and the risk of non-small cell lung cancer
    Oxford University Press (OUP) ; 2008
    In:  Carcinogenesis Vol. 29, No. 11 ( 2008-11), p. 2147-2152
    Details
    In: Carcinogenesis, Oxford University Press (OUP), Vol. 29, No. 11 ( 2008-11), p. 2147-2152
    Type of Medium: Online Resource
    ISSN: 1460-2180 , 0143-3334
    URL: Article
    DOI: 10.1093/carcin/bgn205
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1474206-8
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  • 5
    Online Resource
    Online Resource
    Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection
    Oxford University Press (OUP) ; 2009
    In:  Bioinformatics Vol. 25, No. 9 ( 2009-05-01), p. 1145-1151
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 9 ( 2009-05-01), p. 1145-1151
    Abstract: Motivation: Pathway and gene set-based approaches for the analysis of gene expression profiling experiments have become increasingly popular for addressing problems associated with individual gene analysis. Since most genes are not differently expressed, existing gene set tests, which consider all the genes within a gene set, are subject to considerable noise and power loss, a concern exacerbated in studies in which the degree of differential expression is moderate for truly differentially expressed genes. For a significantly differentially expressed pathway, it is also of substantial interest to select important genes that drive the differential expression of the pathway. Methods: We develop a unified framework to jointly test the significance of a pathway and to select a subset of genes that drive the significant pathway effect. To achieve dimension reduction and gene selection, we decompose each gene pathway into a single score by using a regularized form of linear discriminant analysis, called sparse linear discriminant analysis (sLDA). Testing for the significance of the pathway effect proceeds via permutation of the sLDA score. The sLDA-based test is compared with competing approaches with simulations and two applications: a study on the effect of metal fume exposure on immune response and a study of gene expression profiles among Type II Diabetes patients. Results: Our results show that sLDA-based testing provides a powerful approach to test for the significance of a differentially expressed pathway and gene selection. Availability: An implementation of the proposed sLDA-based pathway test in the R statistical computing environment is available at http://www.hsph.harvard.edu/∼mwu/software/ Contact:  xlin@hsph.harvard.edu Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btp019
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2009
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments
    Oxford University Press (OUP) ; 2007
    In:  Bioinformatics Vol. 23, No. 18 ( 2007-09-15), p. 2441-2448
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 23, No. 18 ( 2007-09-15), p. 2441-2448
    Abstract: Motivation: Mass spectrometry (MS), such as the surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) MS, provides a potentially promising proteomic technology for biomarker discovery. An important matter for such a technology to be used routinely is its reproducibility. It is of significant interest to develop quantitative measures to evaluate the quality and reliability of different experimental methods. Results: We compare the quality of SELDI-TOF MS data using unfractionated, fractionated plasma samples and abundant protein depletion methods in terms of the numbers of detected peaks and reliability. Several statistical quality-control and quality-assessment techniques are proposed, including the Graeco–Latin square design for the sample allocation on a Protein chip, the use of the pairwise Pearson correlation coefficient as the similarity measure between the spectra in conjunction with multi-dimensional scaling (MDS) for graphically evaluating similarity of replicates and assessing outlier samples; and the use of the reliability ratio for evaluating reproducibility. Our results show that the number of peaks detected is similar among the three sample preparation technologies, and the use of the Sigma multi-removal kit does not improve peak detection. Fractionation of plasma samples introduces more experimental variability. The peaks detected using the unfractionated plasma samples have the highest reproducibility as determined by the reliability ratio. Availability: Our algorithm for assessment of SELDI-TOF experiment quality is available at http://www.biostat.harvard.edu/~xlin Contact:  harezlak@post.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btm346
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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