With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistica...With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.展开更多
There are a variety of classification techniques such as neural network, decision tree, support vector machine and logistic regression. The problem of dimensionality is pertinent to many learning algorithms, and it de...There are a variety of classification techniques such as neural network, decision tree, support vector machine and logistic regression. The problem of dimensionality is pertinent to many learning algorithms, and it denotes the drastic raise of computational complexity, however, we need to use dimensionality reduction methods. These methods include principal component analysis (PCA) and locality preserving projection (LPP). In many real-world classification problems, the local structure is more important than the global structure and dimensionality reduction techniques ignore the local structure and preserve the global structure. The objectives is to compare PCA and LPP in terms of accuracy, to develop appropriate representations of complex data by reducing the dimensions of the data and to explain the importance of using LPP with logistic regression. The results of this paper find that the proposed LPP approach provides a better representation and high accuracy than the PCA approach.展开更多
This paper focuses on the quantitative expression of bacterial regrowth in water distribution system. Considering public health risks of bacterial regrowth,the experiment was performed on a distribution system of sele...This paper focuses on the quantitative expression of bacterial regrowth in water distribution system. Considering public health risks of bacterial regrowth,the experiment was performed on a distribution system of selected area.Physical,chemical,and microbiological parameters such as turbidity,temperature,residual chlorine and pH were measured over a three-month period and correlation analysis was carried out.Combined with principal components analysis(PCA) ,a logistic regression model is developed to predict and diagnose bacterial regrowth and locate the zones with high risks of microbiology in the distribution system.The model gives the probability of bacterial regrowth with the number of heterotrophic plate counts as the binary response variable and three new principal components variables as the explanatory variables.The veracity of the logistic regression model was 90%,which meets the precision requirement of the model.展开更多
基金founded by the National Natural Science Foundation of China(81202283,81473070,81373102 and81202267)Key Grant of Natural Science Foundation of the Jiangsu Higher Education Institutions of China(10KJA330034 and11KJA330001)+1 种基金the Research Fund for the Doctoral Program of Higher Education of China(20113234110002)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine)
文摘With recent advances in biotechnology, genome-wide association study （GWAS） has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression （LR） based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression （PC-LR）, partial least squares-based logistic regression （PLS-LR）, have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism （SNP） set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis. On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.
文摘There are a variety of classification techniques such as neural network, decision tree, support vector machine and logistic regression. The problem of dimensionality is pertinent to many learning algorithms, and it denotes the drastic raise of computational complexity, however, we need to use dimensionality reduction methods. These methods include principal component analysis (PCA) and locality preserving projection (LPP). In many real-world classification problems, the local structure is more important than the global structure and dimensionality reduction techniques ignore the local structure and preserve the global structure. The objectives is to compare PCA and LPP in terms of accuracy, to develop appropriate representations of complex data by reducing the dimensions of the data and to explain the importance of using LPP with logistic regression. The results of this paper find that the proposed LPP approach provides a better representation and high accuracy than the PCA approach.
基金Supported by National Natural Science Foundation of China(No.50878140)Project of Water Pollution Control and Repair(No.2008ZX07317-005)
文摘This paper focuses on the quantitative expression of bacterial regrowth in water distribution system. Considering public health risks of bacterial regrowth,the experiment was performed on a distribution system of selected area.Physical,chemical,and microbiological parameters such as turbidity,temperature,residual chlorine and pH were measured over a three-month period and correlation analysis was carried out.Combined with principal components analysis(PCA) ,a logistic regression model is developed to predict and diagnose bacterial regrowth and locate the zones with high risks of microbiology in the distribution system.The model gives the probability of bacterial regrowth with the number of heterotrophic plate counts as the binary response variable and three new principal components variables as the explanatory variables.The veracity of the logistic regression model was 90%,which meets the precision requirement of the model.
