TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


Image Analysis and Signal Extraction for cDNA Microarray Images

Bergemann, T.L., Laws, R.J., and Zhao L.P., Fred Hutchinson Cancer Research Center, Seattle WA

Microarray technologies are now routinely used to monitor genome-wide expression profiles.  Steps in analyzing microarray data are to visualize the images, inspect intensity values and their variations, and then extract signal data for down-stream analyses.  Due to recent advances, several commercial software packages, such as GenePix, have been developed, and are used routinely in practice.  While these technologies are shown to be functional, there remain many concerns about assumptions required for their use as well as lack of statistical rigor in analyzing noisy signal data.In this talk, I will present methods to overcome hurdles in the image analysis bottleneck.  These methods are incorporated into a software application that is available in the public domain.  The goal of our software is to provide researchers with a tool to visually explore image data and assess their confidence in numerical information generated by the experiment.  Meanwhile, this application is useful for statisticians as a means to explore variability in image data.  Further, I will discuss models to quantify spot signals and their variability.  These models speak to the reliability of array data in a given experiment, accounting for sources of bias and variation.

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