Abstract #300878

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JSM 2003 Abstract #300878
Activity Number: 131
Type: Contributed
Date/Time: Monday, August 4, 2003 : 10:30 AM to 12:20 PM
Sponsor: Biopharmaceutical Section
Abstract - #300878
Title: Joint Estimation of Calibration and Expression for High-Density Oligonucleotide Arrays
Author(s): Ann L. Oberg*+ and Karla V. Ballman and Douglas W. Mahoney and Terry M. Therneau
Companies: Mayo Clinic and Mayo Clinic and Mayo Clinic & Mayo Foundation and Mayo Clinic
Address: Section of Biostatistics, Rochester, MN, 55905-0001,
Keywords: linear mixed-effects model ; random effects ; normalization ; calibration ; high-density oligonucleotide array data
Abstract:

There is an increasing awareness that the analysis of high-density oligonucleotide arrays is better modeled as a holistic rather than a piecemeal process. Affymetrix software summarizes each chip (including scaling, background subtraction, and removal of outliers) separately, and the results of that summarization are "passed forward" to the next stage of analysis. Li (2001) introduced a "model-based" analysis, where all chips for a given experimental condition were fit in a single model, giving a more complete and accurate picture of both data errors and the fit. Chu (2002) recently extended this idea, using a random-effects model to encompass all chips in an experiment at once. For all of these, however, normalization of the data is done as a separate prior process. We propose a method that integrates the normalization, visualized as chip-specific calibration curves based on differential binding characteristics, along with model fitting incorporating experimental design in a unified algorithm.

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