• Quantitative Bio-Science
• /
• v.36 no.1
• /
• pp.23-31
• /
• 2017

Datasets from DNA microarray experiments, which are in the form of large matrices of expression levels of genes, often have missing values. However, the existing statistical methods including the principle components analysis (PCA) and Hotelling's t-test are not directly applicable for the datasets having missing values due to the fact that they assume the observed dataset is complete in general. Many methods have been proposed in previous literature to impute the missing in the observed data. Troyanskaya et al. [1] study the k-nearest neighbor (kNN) imputation, Kim et al. [2] propose the local least squares (LLS) method and Rubin [3] propose the multiple imputation (MI) for missing values. To identify differentially expressed genes, we propose a new testing procedure when the missing exists in the observed data. The proposed procedure uses the Stouffer's z-scores and combines the test results of individual imputed samples, which are dependent to each other. We numerically show that the proposed test procedure based on MI performs better than the existing test procedures based on single imputation (SI) by comparing their ROC curves. We apply the proposed method to analyzing a public microarray data.

• Communications for Statistical Applications and Methods
• /
• v.26 no.3
• /
• pp.325-336
• /
• 2019

In this article we extend the discrete Weibull regression model in the presence of missing data. Discrete Weibull regression models can be adapted to various type of dispersion data however, it is not widely used. Recently Yoo (Journal of the Korean Data and Information Science Society, 30, 11-22, 2019) adapted the discrete Weibull regression model using single imputation. We extend their studies by using multiple imputation also with several various settings and compare the results. The purpose of this study is to address the merit of using multiple imputation in the presence of missing data in discrete count data. We analyzed the seventh Korean National Health and Nutrition Examination Survey (KNHANES VII), from 2016 to assess the factors influencing the variable, 1 month hospital stay, and we compared the results using discrete Weibull regression model with those of Poisson, negative Binomial and zero-inflated Poisson regression models, which are widely used in count data analyses. The results showed that the discrete Weibull regression model using multiple imputation provided the best fit. We also performed simulation studies to show the accuracy of the discrete Weibull regression using multiple imputation given both under- and over-dispersed distribution, as well as varying missing rates and sample size. Sensitivity analysis showed the influence of mis-specification and the robustness of the discrete Weibull model. Using imputation with discrete Weibull regression to analyze discrete data will increase explanatory power and is widely applicable to various types of dispersion data with a unified model.

• Journal of the Korean Data and Information Science Society
• /
• v.14 no.3
• /
• pp.579-590
• /
• 2003

When we analyze incomplete data, i.e., data with missing values, we need treatment for the missing values. A common way to deal with this problem is to delete the cases with missing values. Various other methods have been developed. Among them are EM algorithm and regression algorithm which can estimate missing values and impute the missing elements with the estimated values. In this paper, we introduce multiple imputation software SOLAS which generates multiple data sets and imputes with them.

• The Korean Journal of Applied Statistics
• /
• v.28 no.3
• /
• pp.529-540
• /
• 2015

A cross-over design is frequently used in clinical trials (especially in bioequivalence tests with a parametric method) for the comparison of two treatments. Missing values frequently take place in cross-over designs in the second period. Usually, subjects that have missing values are removed and analyzed. However, it can be unsuitable in clinical trials with a small sample size. In this paper, we compare single imputation methods in a $2{\times}2$ cross-over design when missing values exist in the second period. Additionally, parametric and nonparametric methods are compared after applying single imputation methods. A Monte-Carlo simulation study compares type I error and the power of methods.

• Proceedings of the KAIS Fall Conference
• /
• 2003.11a
• /
• pp.105-110
• /
• 2003

Collaborative filtering is one of the methodologies that are most widely used for recommendation system. It is based on a data matrix of each customer's preferences of products. There could be a lot of missing values in such preference. data matrix. This incomplete data is one of the reasons to deteriorate the accuracy of recommendation system. Multiple imputation method imputes m values for each missing value. It overcomes flaws of single imputation approaches through considering the uncertainty of missing values.. The objective of this paper is to suggest multiple imputation-based collaborative filtering approach for recommendation system to improve the accuracy in prediction performance. The experimental works show that the proposed approach provides better performance than the traditional Collaborative filtering approach, especially in case that there are a lot of missing values in dataset used for recommendation system.

• The Korean Journal of Applied Statistics
• /
• v.24 no.2
• /
• pp.315-321
• /
• 2011

Gene expression microarray data often include multiple missing values. Most gene expression analysis (including gene clustering analysis); however, require a complete data matric as an input. In ordinary clustering methods, just a single missing value makes one abandon the whole data of a gene even if the rest of data for that gene was intact. The quality of analysis may decrease seriously as the missing rate is increased. In the opposite aspect, the imputation of missing value may result in an artifact that reduces the reliability of the analysis. To clarify this contradiction in microarray clustering analysis, this paper compared the accuracy of clustering with and without imputation over several microarray data having different missing rates. This paper also tested the clustering efficiency of several imputation methods including our propose algorithm. The results showed it is worthwhile to check the clustering result in this alternative way without any imputed data for the imperfect microarray data.

• Communications for Statistical Applications and Methods
• /
• v.11 no.2
• /
• pp.399-411
• /
• 2004

A common method of handling nonresponse in sample survey is to delete the cases, which may result in a substantial loss of cases. Thus in certain situation, it is of interest to create a complete set of sample values. In this case, a popular approach is to impute the missing values in the sample by the mean or the median of responders. The difficulty with this method which just replaces each missing value with a single imputed value is that inferences based on the completed dataset underestimate the precision of the inferential procedure. Various suggestions have been made to overcome the difficulty but they might not be appropriate for public-use files where the user has only limited information for about the reasons for nonresponse. In this note, a multiple imputation method is considered to create complete dataset which might be used for all possible inferential procedures without misleading or underestimating the precision.

• Genomics & Informatics
• /
• v.8 no.3
• /
• pp.103-107
• /
• 2010

The imputation of untyped SNPs enables researchers to validate association findings across SNP arrays and also enables them to test a large number of SNPs to reveal the fine structure of the association peak, facilitating interpretation of the results and the location of causal polymorphisms. In this study, we applied the imputation method to a genomewide association study and recapitulated the previously associated gene loci of blood pressure traits in Korean cohorts. A total of 1,827,004 SNPs were imputed by the IMPUTE program, and we conducted a genomewide association study for systolic and diastolic blood pressure. While no SNPs passed the Bonferroni correction p-value (p=$2.74{\times}10^{-8}$ for 1,827,004 SNPs), 12 novel loci for systolic blood pressure and 16 novel loci for diastolic blood pressure were detected by imputed SNPs, with $10^{-5}$ < p-value < $10^{-4}$. Moreover, 7 regions (ATP2B1, 10p15.1, ARHGEF12, ALX4, LIPC, 7q31.1, and TCF7L2) out of 14 genetic loci that were previously reported revealed that the imputed SNPs had lower p-values than those of genotyped SNPs. Moreover, a nonsynonymous SNP in the CSMD1 gene, one of the 14 genes, was found to be associated with systolic blood pressure (p<0.05). These results suggest that the imputation method can facilitate the discovery of novel SNPs as well as enhance the fine structure of the association peak in the loci.

• The Korean Journal of Applied Statistics
• /
• v.24 no.5
• /
• pp.871-881
• /
• 2011

In this paper we propose a logistic regression method to estimate the survival function and the median survival time in interval-censored data. The proposed method is motivated by the data augmentation technique with no sacrifice in augmenting data. In addition, we develop a cross validation criterion to determine the size of data augmentation. We compare the proposed estimator with other existing methods such as the parametric method, the single point imputation method, and the nonparametric maximum likelihood estimator through extensive numerical studies to show that the proposed estimator performs better than others in the sense of the mean squared error. An illustrative example based on a real data set is given.

• Communications for Statistical Applications and Methods
• /
• v.25 no.2
• /
• pp.159-172
• /
• 2018

In many epidemiological studies, missing values in the outcome arise due to censoring. Such censoring is what makes survival analysis special and differentiated from other analytical methods. There are many methods that deal with censored data in survival analysis. However, few studies have dealt with missing covariates in survival data. Furthermore, studies dealing with missing covariates are rare when data are clustered. In this paper, we conducted a simulation study to compare results of several missing data methods when data had clustered multi-structured type with missing covariates. In this study, we modeled unknown baseline hazard and frailty with Bayesian B-Spline to obtain more smooth and accurate estimates. We also used prior information to achieve more accurate results. We assumed the missing mechanism as MAR. We compared the performance of five different missing data techniques and compared these results through simulation studies. We also presented results from a Multi-Center study of Korean IBD patients with Crohn's disease(Lee et al., Journal of the Korean Society of Coloproctology, 28, 188-194, 2012).