ArticleApplied and environmental microbiology2008
Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
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- SNR enhanced high-speed two-photon microscopy using a pulse picker and time gating detection.Scientific reports · 2023Article
- PSMA-targeting TGFβ-insensitive armored CAR T cells in metastatic castration-resistant prostate cancer: a phase 1 trial.Nature medicine · 2022Article
- A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization.Biosensors · 2021Article
- Elemental mapping of labelled biological specimens at intermediate energy loss in an energy-filtered TEM acquired using a direct detection device.Journal of microscopy · 2021Article
- Fluorescence Signal Enhancement in Antibody Microarrays Using Lightguiding Nanowires.Nanomaterials (Basel, Switzerland) · 2021Article
- Simultaneous elimination of Malachite Green, Rhodamine B and Cresol Red from aqueous sample with Sistan sand, optimized by Taguchi L16 and Plackett-Burman experiment design methods.Chemistry Central journal · 2018Article
- High-performance serial block-face SEM of nonconductive biological samples enabled by focal gas injection-based charge compensation.Journal of microscopy · 2018Article
- Elevated COFrontiers in microbiology · 2018Article
- FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota.Frontiers in microbiology · 2018Article
- Divergent Responses of Forest Soil Microbial Communities under Elevated COApplied and environmental microbiology · 2018Article
- Development and validation of a custom microarray for global transcriptome profiling of the fungus Aspergillus nidulans.Current genetics · 2016Article
- Gene expression prediction using low-rank matrix completion.BMC bioinformatics · 2016Article
- Shrink-induced silica multiscale structures for enhanced fluorescence from DNA microarrays.Langmuir : the ACS journal of surfaces and colloids · 2014Article
- Microarray-based gene expression profiling to elucidate effectiveness of fermented Codonopsis lanceolata in mice.International journal of molecular sciences · 2014Article
- Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem.The ISME journal · 2014Article
- Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone.The ISME journal · 2013Article
- Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands.Applied and environmental microbiology · 2013Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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 the signal-to-both-standard-deviations ratio (SSDR), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (SSR) and the signal-to-background ratio (SBR). At a low stringency, the thresholds of the SSR, SBR, and SSDR were 2.5, 1.60, and 0.80 with an oligonucleotide and a PCR amplicon as target templates and 2.0, 1.60, and 0.70 with genomic DNAs as target templates. Slightly higher thresholds were obtained under high-stringency conditions. The thresholds of the 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 compositions of targets, while the SBR remained unchanged in all situations. The lowest percentage of false positives and false negatives 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.
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