Fall Seminar Series - November 10, 2005
University of Minnesota
School of Statistics
College of Liberal Arts
Signal
Quality Measurements for cDNA Microarray Data
Tracy L. Bergemann
Division of Biostatistics
University of Minnesota
Thursday, November 10, 2005
3:30 PM, 115
Ford Hall
Minneapolis, East Bank Campus
Social at 3:00 PM, 300 Ford Hall
Abstract
Concerns about the reliability of transcription rates estimates derived
from microarray data inspires ongoing research into measurement error
in these experiments. Error happens at both the technical level within
the lab and the experimental level. In this paper, we are concerned
with measuring spot-specific error.
This paper outlines two different approaches to quantify the
reliability of spot-specific intensity estimates. In both cases, the
spatial correlation between pixels and its impact on spot quality is
accounted for. The first method is a straightforward parametric
estimate of within-spot variance that assumes a Gaussian distribution
and accounts for spatial correlation via an overdispersion factor. The
second method employs a non-parametric quality estimate referred to
throughout as the mean square prediction error (MSPE). The MSPE first
smooths a pixel region and then measures the difference between actual
pixel values and the smoother.
Both methods herein are compared for real and simulated data to assess
numerical characteristics and the ability to describe poor spot
quality. Further, we examine the use of spot quality estimates to
increase efficiency in downstream analysis.