JSM 2005 - Toronto

Abstract #304793

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Legend: = Applied Session, = Theme Session, = Presenter
Activity Number: 277
Type: Contributed
Date/Time: Tuesday, August 9, 2005 : 10:30 AM to 12:20 PM
Sponsor: Biometrics Section
Abstract - #304793
Title: The Analysis of Oligonucleotide Microarray Data at the Raw Image Level
Author(s): Jeff Palmer*+
Companies: Carnegie Mellon University
Address: 4950 Bayard St, Pittsburgh, PA, 15213, United States
Keywords: oligonucleotide microarray ; image registration ; interpolation ; feature extraction
Abstract:

In a typical oligonucleotide microarray experiment, the quantification of gene expression levels from the physical medium of the microarray involves several intermediate steps. One of these preprocessing steps is that of extracting the oligonucleotide probe intensity values, or features, from the raw scanned image. For Affymetrix GeneChip microarrays, this step typically is performed by first aligning a global grid to the image that identifies candidate pixel locations corresponding to the centers of the probes. These candidate locations are then allowed to vary locally by a few pixels in each direction, and a final estimate of the feature center is that which yields the smallest coefficient of variation in the surrounding pixels. Empirical evidence has shown the true probe boundaries will typically not match the estimated boundaries imposed by this gridding algorithm. Reasons for this include the array being rotated slightly in the image, the landmarks used for gridding being incorrectly determined, and the image resolution yielding features with noninteger pixel dimensions. An alternative feature extraction algorithm is proposed that circumvents these issues.

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