PHS researchers develops a better array-technology research tool

Brief
October 2, 2003

Researchers in the Public Health Sciences Division have developed a new tool for analyzing microarray image data.

Richard Laws, Tracy Bergemann and Dr. Lue Ping Zhao report the development of the analytic tool and related software application, known as SignalViewer, in the Sept. 1 issue of Bioinformatics. The tool is designed to analyze image data from cDNA microarrays.

A key feature of the software is user-friendliness for biologists, biostatisticians and computer scientists who wish to analyze image data acquired from cDNA microarrays and inspect the quality of processed chip data, before carrying out downstream-data analysis.

Other features of this software tool include:

• Aligning"spots" automatically
• Processing image data in batches
• Allowing users to visualize the image data of the entire array, or a selected block of spots, or even pixel data within a single spot
• Producing rigorously assessed expression values with estimated standard errors and with meaningful flags

Zhao said that one user has described SignalViewer as allowing him to have views of the "forest" (entire chip), "tree" (block of spots), and "branches" (individual spots), at his fingertips.

Bergemann, a graduate student at the University of Wash-ington, contributed to this project by developing improved statistical measurements for the quality of individual gene expression values as part of her dissertation work with Dr. Zhao.

SignalViewer is now freely available to all academic users from the following Web site: http://qge.fhcrc.org/signal/viewer.

Zhao said that since information about the software has been published, the number of people downloading SignalViewer has increased significantly, indicating that many researchers are exploring whether SignalViewer may be helpful to their array-technology research.

"We're pleased to see that our work is contributing to the biomedical community in some way," he said.

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