Actions for Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis [electronic resource].

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Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis [electronic resource].

Published
Berkeley, Calif. : Lawrence Berkeley National Laboratory, 2008.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy.
Physical Description
41 : digital, PDF file
Additional Creators
Lawrence Berkeley National Laboratory and United States. Department of Energy. Office of Scientific and Technical Information
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Summary
Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called signal to both standard deviations ratio (SSDR) was developed, and evaluated along with other two methods, signal to standard deviation ratio (SSR), and signal to background ratio (SBR). At a low stringency, the thresholds of SSR, SBR, and SSDR were 2.5, 1.60 and 0.80 with oligonucleotide and PCR amplicon as target templates, and 2.0, 1.60 and 0.70 with genomic DNA as target templates. Slightly higher thresholds were obtained at the high stringency condition. The thresholds of SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types), and the presence of background DNA, and a decrease in the composition of targets, while SBR remained unchanged under all situations. The lowest percentage of false positives (FP) and false negatives (FN) was observed with the SSDR calculation method, suggesting that it may be a better SNR calculation for more accurate determination of SNR thresholds. Positive spots identified by SNR thresholds were verified by the Student t-test, and consistent results were observed. This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions.
Report Numbers
E 1.99:lbnl-538e
lbnl-538e
Other Subject(s)
Note
Published through SciTech Connect.
03/06/2008.
"lbnl-538e"
Applied and Environmental Microbiology 74 10 ISSN 0099-2240; AEMIDF FT
Zhou, Jizhong; He, Zhili.
Funding Information
DE-AC02-05CH11231
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