IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v9y2010i1n14.html
   My bibliography  Save this article

An Internal Calibration Method for Protein-Array Studies

Author

Listed:
  • Daly Don Simone

    (Pacific Northwest National Laboratory)

  • Anderson Kevin K

    (Pacific Northwest National Laboratory)

  • Seurynck-Servoss Shannon L

    (University of Arkansas)

  • Gonzalez Rachel M

    (University of Washington)

  • White Amanda M

    (Pacific Northwest National Laboratory)

  • Zangar Richard C

    (Pacific Northwest National Laboratory)

Abstract

Nuisance factors in a protein-array study add obfuscating variation to spot intensity measurements, diminishing the accuracy and precision of protein concentration predictions. The effects of nuisance factors may be reduced by design of experiments, and by estimating and then subtracting nuisance effects. Estimated nuisance effects also inform about the quality of the study and suggest refinements for future studies.We demonstrate a method to reduce nuisance effects by incorporating a non-interfering internal calibration in the study design and its complemental analysis of variance. We illustrate this method by applying a chip-level internal calibration in a biomarker discovery study.The variability of sample intensity estimates was reduced 16% to 92% with a median of 58%; confidence interval widths were reduced 8% to 70% with a median of 35%. Calibration diagnostics revealed processing nuisance trends potentially related to spot print order and chip location on a slide.The accuracy and precision of a protein-array study may be increased by incorporating a non-interfering internal calibration. Internal calibration modeling diagnostics improve confidence in study results and suggest process steps that may need refinement. Though developed for our protein-array studies, this internal calibration method is applicable to other targeted array-based studies.

Suggested Citation

  • Daly Don Simone & Anderson Kevin K & Seurynck-Servoss Shannon L & Gonzalez Rachel M & White Amanda M & Zangar Richard C, 2010. "An Internal Calibration Method for Protein-Array Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-23, January.
    • Handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:14
    DOI: 10.2202/1544-6115.1506
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1506
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1506?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Daly Don Simone & Anderson Kevin K & White Amanda M & Gonzalez Rachel M & Varnum Susan M & Zangar Richard C, 2008. "Predicting Protein Concentrations with ELISA Microarray Assays, Monotonic Splines and Monte Carlo Simulation," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-21, July.
    2. Thilakarathne Pushpike J & Verbeke Geert & Engelen Kristof & Marchal Kathleen, 2009. "A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-27, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lim Johan & Kim Jayeon & Kim Byung Soo, 2010. "An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-12, January.

    More about this item

    Keywords

    protein array; internal calibration;

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:14. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.