Journal of biometrics & biostatistics最新文献_第9页

Inference and Sample Size Calculations Based on Statistical Tests in aNegative Binomial Distribution for Differential Gene Expression in RNAseqData 基于RNAseqData中差异基因负二项分布统计检验的推断和样本量计算

Journal of biometrics & biostatistics Pub Date : 2017-01-30 DOI: 10.4172/2155-6180.1000332

Xiaohong Li, N. Cooper, Y. Shyr, Dongfeng Wu, E. Rouchka, R. Gill, T. O’Toole, G. Brock, S. Rai

{"title":"Inference and Sample Size Calculations Based on Statistical Tests in aNegative Binomial Distribution for Differential Gene Expression in RNAseqData","authors":"Xiaohong Li, N. Cooper, Y. Shyr, Dongfeng Wu, E. Rouchka, R. Gill, T. O’Toole, G. Brock, S. Rai","doi":"10.4172/2155-6180.1000332","DOIUrl":"https://doi.org/10.4172/2155-6180.1000332","url":null,"abstract":"The high throughput RNA sequencing (RNA-seq) technology has become the popular method of choice for transcriptomics and the detection of differentially expressed genes. Sample size calculations for RNA-seq experimental design are an important consideration in biological research and clinical trials. Currently, the sample size formulas derived from the Wald and the likelihood ratio statistical tests with a Poisson distribution to model RNA-seq data have been developed. However, since the mean read counts in the real RNA-seq data are not equal to the variance, an extended method to calculate sample sizes based on a negative binomial distribution using an exact test statistic was proposed by Li et al. in 2013. In this study, we alternatively derive five sample size calculation methods based on the negative binomial distribution using the Wald test, the log-transformed Wald test and the log-likelihood ratio test statistics. A comparison of our five methods and an existing method was performed by calculating the sample sizes and the simulated power in different scenarios. We first calculated the sample sizes for testing a single gene using the six methods given a nominal significance level α at 0.05 and 80% power. Then, we calculated the sample sizes for testing multiple genes given a false discovery rate (FDR) at 0.05 and 0.10. The empirical power and true prognostic genes for differential gene expression analysis corresponding to the estimated sample sizes from the six methods are also estimated via the simulation studies. Using the sample size formulas derived from log-transformed and Wald-based tests, we observed smaller sample properties while maintaining the nominal power close to or higher than 80% in all the settings compared to other methods. Moreover, the Wald test based sample size calculation method is easier to compute and faster in an RNA-seq experimental design.","PeriodicalId":87294,"journal":{"name":"Journal of biometrics & biostatistics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42416088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Bayesian Regression Analysis of Correlates of Modern ContraceptiveMethod Usage: A Case Study in Hawassa City, Ethiopia 现代避孕方法使用相关性的贝叶斯回归分析——以埃塞俄比亚哈瓦萨市为例

Journal of biometrics & biostatistics Pub Date : 2017-01-09 DOI: 10.4172/2155-6180.1000330

G. Kiros

引用次数: 0

Fast Computation of Significance Threshold in QTL Mapping of DynamicQuantitative Traits 动态数量性状QTL定位中显著性阈值的快速计算

Journal of biometrics & biostatistics Pub Date : 2017-01-09 DOI: 10.4172/2155-6180.1000329

Nating Wang, H. Tian, Yongci Li, R. Wu, Jiangtao Luo, Zhong Wang

引用次数: 2

Body Image and Media 身体形象与媒体

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000368

N. Khan

引用次数: 3

Human and Hummingbird Hemoglobin Concentrations and MetabolicRhythms at Altitude Determined with Statistical Modeling 人类和蜂鸟血红蛋白浓度和代谢节律在海拔与统计模型确定

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000373

C. Qualls, C. Witt, Nicholas R. Wilson, Sebastian Restrepo Cruz, Emil Bautista, O. Appenzeller

{"title":"Human and Hummingbird Hemoglobin Concentrations and MetabolicRhythms at Altitude Determined with Statistical Modeling","authors":"C. Qualls, C. Witt, Nicholas R. Wilson, Sebastian Restrepo Cruz, Emil Bautista, O. Appenzeller","doi":"10.4172/2155-6180.1000373","DOIUrl":"https://doi.org/10.4172/2155-6180.1000373","url":null,"abstract":"Hummingbirds show remarkable adaptation to high altitude hypoxia whereas humans are imperfectly adapted to high altitude living. Here we compare hemoglobin levels and metabolism derived from growth rhythms in hummingbirds and humans. To compare growth rhythms, we analyzed growth intervals in hummingbird tail feathers and human growing tissues such as hair. We find that hemoglobin levels were higher in hummingbirds (P<0.001) than in humans, but the influence of altitude on hemoglobin was more pronounced in humans (slope, steeper with increasing altitude, P<0.001), and levels for both taxa converge at extreme elevations. The power spectra from growth intervals in growing tissues which reflect metabolism in both species, were not different (low frequency/high frequency ratios (LF/HF) in the two species) P>0.22 NS. In a comparison among hummingbird species, we found no evidence that metabolic demands (based on power spectra derived from growth intervals) changed with increasing altitude, even while body mass increased significantly (P>0.02). Our index of hummingbird metabolism (spectral LF/HF ratio) was consistent with estimates based on allometric conversion of mass for humans. These results support the notion that hummingbird hemoglobin levels and metabolism are useful models for biologically adaptive strategies to life at high altitude. Humans and hummingbirds exhibit convergent phenotypes for hemoglobin concentration at extreme altitudes. However, whereas human health suffers above 2500 m, hummingbirds are evolutionarily successful and physiologically robust at very high altitudes. Such different outcomes may be in part due to ancient versus recent high altitude colonization, but may also reflect greater altitude-specialization of hummingbird species, fundamental differences between avian and mammalian respiratory systems, or the very different demands of thermoregulation in hummingbirds versus humans.","PeriodicalId":87294,"journal":{"name":"Journal of biometrics & biostatistics","volume":"8 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70291744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Spatial Autocorrelation in Voting Turnout 投票率的空间自相关

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000376

Mahdi-Salim Saib

引用次数: 5

Dose Finding for Drug Combination in Early Cancer Phase I Trials using Conditional Continual Reassessment Method. 使用条件连续重新评估方法寻找早期癌症I期临床试验中药物联合的剂量。

Journal of biometrics & biostatistics Pub Date : 2017-01-01 Epub Date: 2017-11-27 DOI: 10.4172/2155-6180.1000381

Márcio Augusto Diniz, Quanlin-Li, Mourad Tighiouart

{"title":"Dose Finding for Drug Combination in Early Cancer Phase I Trials using Conditional Continual Reassessment Method.","authors":"Márcio Augusto Diniz, Quanlin-Li, Mourad Tighiouart","doi":"10.4172/2155-6180.1000381","DOIUrl":"https://doi.org/10.4172/2155-6180.1000381","url":null,"abstract":"<p><p>We describe a dose escalation algorithm for drug combinations in cancer phase I clinical trials. Parametric models for describing the association between the doses and the probability of dose limiting toxicity are used assuming univariate monotonicity of the dose-toxicity relationship. Trial design proceeds using the continual reassessment method, where at each stage of the trial, we seek the dose of one agent with estimated probability of toxicity closest to a target probability of toxicity given the current dose of the other agent. A Bayes estimate of the maximum tolerated dose (MTD) curve is proposed at the conclusion of the trial for continuous doses or a set of MTDs is determined in the case of discrete dose levels. We evaluate design operating characteristics in terms of safety of the trial and percent of dose recommendation at dose combination neighborhoods around the true MTD under various model generated scenarios and misspecification. The method is further assessed for varying algorithms enrolling cohorts of two and three patients receiving different doses and compared to previous approaches such as escalation with overdose control and two-dimensional design.</p>","PeriodicalId":87294,"journal":{"name":"Journal of biometrics & biostatistics","volume":"8 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/2155-6180.1000381","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35924986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Determination of Association between Duration of Labour and Some Social Status Using Chi-Square Distribution (χ 2 ) 用卡方分布确定劳动时间与某些社会地位的关系(χ 2)

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000372

O. Peter, Iornongo Ag

引用次数: 0

Tooth Growth in Ancient and Modern Times Inferred from Perikymata Growth Intervals; Modeled Statistically 由外突生长时间推断古今牙齿生长统计建模

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000380

C. Qualls, M. A. Costa, M. Paffett, O. Appenzeller

引用次数: 1

Audio-Visual Person Recognition Using Deep Convolutional Neural Networks 基于深度卷积神经网络的视听人物识别

Journal of biometrics & biostatistics Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000377

Sagar Vegad, H. Patel, H. Zhuang, M. Naik

引用次数: 7