Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis
Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis
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DOI：
10.1128/aem.02536-07
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发表时间：
2008-05-01
影响因子：
4.4
通讯作者：
Zhou, Jizhong
中科院分区：
文献类型：
--
作者：
He, Zhili;Zhou, Jizhong
微阵列数据分析的信噪比（SNR）阈值通过实验确定与寡核苷酸阵列，其中包含完全匹配（PM）和错配（MM）探针的基础上从希瓦氏菌oneidensis MR-1的四个基因。提出了一种新的信噪比计算方法，称为信号与双标准偏差比（SSDR），并与另外两种方法，信号与标准偏差比（SSR）和信号与背景比（SBR）一起进行了沿着评估。在低严格度下，以寡核苷酸和PCR扩增子为目标模板时，SSR、SBR和SSDR的阈值分别为2.5、1.60和0.80，以基因组DNA为目标模板时，阈值分别为2.0、1.60和0.70。在高严格性条件下获得了略高的阈值。SSR和SSDR的阈值随着目标复杂性的增加而降低（例如，目标类型）和背景DNA的存在以及目标组成的减少，而SBR在所有情况下保持不变。使用SSDR计算方法观察到最低的假阳性和假阴性百分比，这表明它可能是用于更准确地确定SNR阈值的更好的SNR计算。通过Student t检验验证通过SNR阈值鉴定的阳性斑点，并观察到一致的结果。该研究为用户在不同杂交条件下为不同样本选择合适的信噪比阈值提供了一般性指导。
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.