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Abstract
In the article, Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr. Pozhitkov used the Scanner Calibration Slide, a key product of Full Moon BioSystems to generate data in his study of microarray scanner PMT response and proposed a mathematic model for PMT response [1]. In the end, the author concluded that "Full Moon BioSystems calibration slides are inadequate for performing calibration," and recommended "against using these slides." We found these conclusions are seriously flawed and misleading, and his recommendation against using the Scanner Calibration Slide was not properly supported.
Highlights
To scanner users, the most important goal is to correctly quantify a feature on a microarray image and determine whether the signal intensity, an arbitrary reading from the scanner, is a real signal, which is directly affected by noise and other background variations [2]
The Scanner Calibration Slide was designed by Full Moon BioSystems to simulate real microarray chips, which are comprised of substrates, printing buffer and printed material
The Scanner Calibration Slide allows users to establish a working curve using a simple dilution series of fluorescent material printed on the slide, to asses microarray scanner’s general performance, and to evaluate and compare multiple scanner systems
Summary
The most important goal is to correctly quantify a feature on a microarray image and determine whether the signal intensity, an arbitrary reading from the scanner, is a real signal, which is directly affected by noise and other background variations [2]. The Scanner Calibration Slide allows users to establish a working curve using a simple dilution series of fluorescent material printed on the slide, to asses microarray scanner’s general performance, and to evaluate and compare multiple scanner systems. In Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr Pozhitkov used the Scanner Calibration Slide to generate a series of data in effort to analyze PMT response in microarray scanners [1] He chose not to follow the product instructions in utilizing. In his study, using the data generated by the Scanner Calibration Slides, Dr Pozhitkov established several working curves to analyze PMT response. The plateau in the working curve established by the Scanner Calibration Slide indicates the scanner response has reached its limit of detection and can no longer discriminate the difference in fluorescent signals. The results and conclusion from this kind of contradicting study cannot be trusted
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