• Genomics & Informatics
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• v.6 no.4
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• pp.231-234
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• 2008

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile normalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA backgroundcorrection resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.51-56
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• 2005

There are many sources of systematic variations in cDNA microarray experiments which affect the measured gene expression levels like differences in labeling efficiency between the two fluorescent dyes. Print-tip lowess normalization is used in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. However, print-tip lowess normalization performs poorly in situation where error variability for each gene is heterogeneous over intensity ranges. We proposed the new print-tip normalization methods based on support vector machine regression(SVMR) and support vector machine quantile regression(SVMQR). SVMQR was derived by employing the basic principle of support vector machine (SVM) for the estimation of the linear and nonlinear quantile regressions. We applied our proposed methods to previous cDNA micro array data of apolipoprotein-AI-knockout (apoAI-KO) mice, diet-induced obese mice, and genistein-fed obese mice. From our statistical analysis, we found that the proposed methods perform better than the existing print-tip lowess normalization method.

• Journal of Information Technology Applications and Management
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• v.25 no.1
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• pp.67-85
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• 2018

We propose a noise reduced risk aversion index for measuring risk aversion through a laboratory experiment to overcome disadvantages of the multiple pricing list format developed by Holt and Laury (2002). We use randomized multiple list choices with coarser classification and reward weighting, supplement the rank of risk aversion with extra individual characteristics of risk attitude, and construct an index of risk aversion by standardizing the risk aversion ranking with quantile normalization. Our method reduces multiple switching problems that noisy decision makers mistakenly commit in experimental approaches, so that it is free of the framing effect which severely occurred in the HL. Furthermore, the index doesn't utilize any specific utility function or probability weighting, which allows researcher to hold the independence axiom. Since our noise reduced index of risk aversion has many good traits, it is widely used and applied to reveal fundamental characteristics of risk-related behaviors in economics and finance regardless of experimental environment.

• Journal of the Korean Data and Information Science Society
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• v.18 no.4
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• pp.1005-1021
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• 2007

Traditional procedures for DNA microarray data analysis are to preprocess and normalize the gene expression data, and then to analyze the normalized data using statistical tests. Drawbacks of the traditional methods are: genuine biological signal may be unwillingly eliminated together with artifacts, the limited number of arrays per gene make statistical tests difficult to use the normality assumption or nonparametric method, and genes are tested independently without consideration of interrelationships among genes. A novel method using average rank in each array is proposed to eliminate such drawbacks. This average rank method monitors differentially regulated genes among genetically different groups and the selected genes are somewhat different from those selected by traditional P-value method. Addition of genes selected by the average rank method to the traditional method will provide better understanding of genetic differences of groups.

• Journal of the Korea Convergence Society
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• v.10 no.10
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• pp.7-13
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• 2019

The natural gas (NG), mostly methane leaks into the air, it is a big problem for the climate. detected NG leaks under U.S. city streets and collected data. In this paper, we introduced a Deep Neural Network (DNN) classification of prediction for a level of NS leak. The proposed method is OrdinalEncoder(OE) based K-means clustering and Multilayer Perceptron(MLP) for predicting NG leak. The 15 features are the input neurons and the using backpropagation. In this paper, we propose the OE method for labeling target data using k-means clustering and compared normalization methods performance for NG leak prediction. There five normalization methods used. We have shown that our proposed OE based MLP method is accuracy 97.7%, F1-score 96.4%, which is relatively higher than the other methods. The system has implemented SPSS and Python, including its performance, is tested on real open data.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.14 no.2
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• pp.534-539
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• 2010

In genomic studies, thousands of features are collected on relatively few samples. One of the goals of these studies is to build classifiers to predict the outcome of future observations. There are three inherent steps to build classifiers: a significant gene selection, model selection and prediction assessment. In the paper, with a focus on prediction assessment, we normalize microarray data with quantile-normalization methods that adjust quartile of all slide equally and then design a system comparing several methods to estimate 'true' prediction error of a prediction model in the presence of feature selection and compare and analyze a prediction error of them. LOOCV generally performs very well with small MSE and bias, the split sample method and 2-fold CV perform with small sample size very pooly. For computationally burdensome analyses, 10-fold CV may be preferable to LOOCV.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.29 no.4B
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• pp.319-328
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• 2009

This study quantified the data by applying the EDA techniques considering the data structure, and the results were then used for the frequency analysis. Although traditional methods based on the method of moments provide very sensitive statistics to the extreme values, the EDA techniques have an advantage of providing very stable statistics with their small variation. For the application of the EDA techniques to the frequency analysis, it is necessary to normalization transform and inverse-transform to conserve the skewness of the raw data. That is, it is necessary to transform the raw data to make the data follow the normal distribution, to estimate the statistics by applying the EDA techniques, and then finally to inverse-transform the statistics of transformed data. These statistics decided are then applied for the frequency analysis with a given probability density function. This study analyzed the annual maxima one hour rainfall data at Seoul and Pohang stations. As a result, it was found that more stable rainfall quantiles, which were also less sensitive to extreme values, could be estimated by applying the EDA techniques. This methodology may be effectively used for the frequency analysis of rainfall at stations with especially high annual variations of rainfall due to climate change, etc.