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  • Oxford University Press (OUP)  (2)
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  • Oxford University Press (OUP)  (2)
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  • 1
    Online Resource
    Online Resource
    GlobalANCOVA: exploration and assessment of gene group effects
    Oxford University Press (OUP) ; 2008
    In:  Bioinformatics Vol. 24, No. 1 ( 2008-01-01), p. 78-85
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 1 ( 2008-01-01), p. 78-85
    Abstract: Motivation: Several authors have studied expression in gene sets with specific goals: overrepresentation of interesting genes in functional groups, predictive power for class membership and searches for groups where the constituent genes show coordinated changes in expression under the experimental conditions. The purpose of this article is to follow the third direction. One important aspect is that the gene sets under analysis are known a priori and are not determined from the experimental data at hand. Our goal is to provide a methodology that helps to identify the relevant structural constituents (phenotypical, experimental design, biological component) that determine gene expression in a group. Results: Gene-wise linear models are used to formalize the structural aspects of a study. The full model is contrasted with a reduced model that lacks the relevant design component. A comparison with respect to goodness of fit is made and quantified. An asymptotic test and a permutation test are derived to test the null hypothesis that the reduced model sufficiently explains the observed expression within the gene group of interest. Graphical tools are available to illustrate and interpret the results of the analysis. Examples demonstrate the wide range of application. Availability: The R-package GlobalAncova (http://www.bioconductor.org) offers data and functions as well as a vignette to guide the user through specific analysis steps. Contact:  hummel@ibe.med.uni-muenchen.de
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btm531
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    TEQC: an R package for quality control in target capture experiments
    Oxford University Press (OUP) ; 2011
    In:  Bioinformatics Vol. 27, No. 9 ( 2011-05-01), p. 1316-1317
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 27, No. 9 ( 2011-05-01), p. 1316-1317
    Abstract: Summary:  TEQC is an R/Bioconductor package for quality assessment of target enrichment experiments. Quality measures comprise specificity and sensitivity of the capture, enrichment, per-target read coverage and its relation to hybridization probe characteristics, coverage uniformity and reproducibility, and read duplicate analysis. Several diagnostic plots allow visual inspection of the data quality. Availability and implementation:  TEQC is implemented in the R language (version & gt;2.12.0) and is available as a Bioconductor package for Linux, Windows and MacOS from www.bioconductor.org. Contact:  manuela.hummel@crg.es
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btr122
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
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    Online Resource
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    Availability (electronic / print)
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