Biometrical Letters最新文献

筛选
英文 中文
Application of edgeR and DESeq2 methods in plant experiments based on RNA-seq technology 基于RNA-seq技术的edgeR和DESeq2方法在植物实验中的应用
Biometrical Letters Pub Date : 2022-12-01 DOI: 10.2478/bile-2022-0009
Grażyna Niedziela, Alicja Szabelska-Beręsewicz, J. Zyprych-Walczak, M. Graczyk
{"title":"Application of edgeR and DESeq2 methods in plant experiments based on RNA-seq technology","authors":"Grażyna Niedziela, Alicja Szabelska-Beręsewicz, J. Zyprych-Walczak, M. Graczyk","doi":"10.2478/bile-2022-0009","DOIUrl":"https://doi.org/10.2478/bile-2022-0009","url":null,"abstract":"Summary We compared two of the most common methods for differential expression analysis in the RNA-seq field: edgeR and DESeq2. We evaluated these methods based on four real RNA-seq plant datasets. The results indicate that there is a large number of joint differentially expressed genes between the two methods. However, depending on the research goal and the preparation of an experiment, different approaches to statistical analysis and interpretation of the results can be suggested. We focus on answering the question: what workflow should be used in the statistical analysis of the datasets under consideration to minimize the number of falsely identified differentially expressed genes?","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82277544","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: 1
Classification methods in the diagnosis of breast cancer 分类方法在乳腺癌诊断中的应用
Biometrical Letters Pub Date : 2022-12-01 DOI: 10.2478/bile-2022-0008
Anna Magdalena Ogłoszka, Łukasz Smaga
{"title":"Classification methods in the diagnosis of breast cancer","authors":"Anna Magdalena Ogłoszka, Łukasz Smaga","doi":"10.2478/bile-2022-0008","DOIUrl":"https://doi.org/10.2478/bile-2022-0008","url":null,"abstract":"Summary This paper concerns the problem of diagnosing the type of cancer with the use of machine learning and statistical methods. Nowadays, the problem of neoplasms, in particular breast cancer, is one of humanity's greatest challenges. The identification of cancer and its type is extremely important. In solving this problem, classification methods can be used as objective tools that may be helpful for doctors making a diagnosis. For this reason, we discuss many efficient classifiers in the context of cancer detection. In addition, we consider the topic of data set transformations to deal with the problem of data unbalance, as well as measures of classification quality. In the experimental part, an attempt will be made to find the best classifier and to improve the quality of the original data set to obtain the highest values of classification quality measures for a particular data set.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75991319","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: 0
Structures of the covariance matrix: An overview 协方差矩阵的结构:概述
Biometrical Letters Pub Date : 2022-12-01 DOI: 10.2478/bile-2022-0010
Malwina Janiszewska
{"title":"Structures of the covariance matrix: An overview","authors":"Malwina Janiszewska","doi":"10.2478/bile-2022-0010","DOIUrl":"https://doi.org/10.2478/bile-2022-0010","url":null,"abstract":"Summary In this paper, some multivariate and double multivariate modelling approaches are presented. Moreover, this article provides an overview of the modelling of the structure of the covariance matrix. Furthermore, some methods of covariance structure identification are given.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83905032","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: 0
Computing analytic Bayes factors from summary statistics in repeated-measures designs 从重复测量设计的汇总统计计算分析贝叶斯因子
Biometrical Letters Pub Date : 2022-09-16 DOI: 10.2478/bile-2023-0001
Thomas J. Faulkenberry, Keelyn B. Brennan
{"title":"Computing analytic Bayes factors from summary statistics in repeated-measures designs","authors":"Thomas J. Faulkenberry, Keelyn B. Brennan","doi":"10.2478/bile-2023-0001","DOIUrl":"https://doi.org/10.2478/bile-2023-0001","url":null,"abstract":"Summary Bayes factors are an increasingly popular tool for indexing evidence from experiments. For two competing population models, the Bayes factor reflects the relative likelihood of observing some data under one model compared to the other. Computing Bayes factors can be difficult, requiring one to integrate the product of the likelihood and a prior distribution on the population parameter(s) for both competing models. Previous work has obviated this difficulty for independent-groups designs. In this paper, we develop a new analytic formula for computing Bayes factors directly from minimal summary statistics in repeated-measures designs. This work is an improvement on previous methods for computing Bayes factors from summary statistics (e.g., the BIC method), which produce Bayes factors that violate the Sellke upper bound of evidence for smaller sample sizes. The new approach taken in this paper requires knowing only the F -statistic and degrees of freedom, both of which are commonly reported in most empirical work. In addition to providing computational examples, we report a simulation study that benchmarks the new formula against other methods for computing Bayes factors in repeated-measures designs. Our new method provides an easy way for researchers to compute Bayes factors directly from a minimal set of summary statistics, allowing users to index the evidential value of their own data, as well as data reported in published studies.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89301212","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: 2
On a construction procedure for split-block-plot designs based on the Khatri–Rao product of incidence matrices 基于关联矩阵Khatri-Rao积的分块图设计构造方法
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0005
K. Ambroży-Deręgowska, I. Mejza
{"title":"On a construction procedure for split-block-plot designs based on the Khatri–Rao product of incidence matrices","authors":"K. Ambroży-Deręgowska, I. Mejza","doi":"10.2478/bile-2022-0005","DOIUrl":"https://doi.org/10.2478/bile-2022-0005","url":null,"abstract":"Summary The construction of incomplete split-block-plot (SBP) designs for three-factor experiments is investigated. A semi-Kronecker (Khatri–Rao) product of matrices is used in the construction procedure. With this method some generated designs are obtained where column treatments and subplot treatments are allocated in balanced square lattice designs, while row treatments are in a randomized complete block design. Experiments with an orthogonal block structure are considered. In this paper we consider designs which are generally balanced. This allows us to give the stratum efficiency factors for treatment combination contrasts in the proposed split-block-plot designs.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85732596","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: 0
Maximum Likelihood and L2 Environmental Indices in Joint Regression Analysis 联合回归分析中的最大似然与L2环境指数
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0003
D. G. Pereira
{"title":"Maximum Likelihood and L2 Environmental Indices in Joint Regression Analysis","authors":"D. G. Pereira","doi":"10.2478/bile-2022-0003","DOIUrl":"https://doi.org/10.2478/bile-2022-0003","url":null,"abstract":"Summary This paper describes an iterative analysis of incomplete genotype × environment data. L2 environmental indices were introduced to enable the use of Joint Regression Analysis (JRA) in analyzing experiments with incomplete blocks. We now show how, once normality of yields is assumed, the introduction of L2 environmental indices provides a theoretical framework for Joint Regression Analysis. Using this framework, maximum likelihood estimators are obtained and likelihood ratio tests are derived. It is noted that the technique allows unequal weighting of data, and the special case of complete blocks is discussed.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87504630","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: 0
Contribution to spring balance weighing designs 对弹簧秤称重设计的贡献
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0004
M. Graczyk, B. Ceranka
{"title":"Contribution to spring balance weighing designs","authors":"M. Graczyk, B. Ceranka","doi":"10.2478/bile-2022-0004","DOIUrl":"https://doi.org/10.2478/bile-2022-0004","url":null,"abstract":"Summary In this paper, we present some new results regarding spring balance weighing designs. We consider issues with regard to conditions for the existence of optimal designs, and give examples of optimal designs.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75377135","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: 1
Considering distance measures in Statistics 考虑到统计学中的距离度量
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0006
C. Kitsos, C. Nisiotis
{"title":"Considering distance measures in Statistics","authors":"C. Kitsos, C. Nisiotis","doi":"10.2478/bile-2022-0006","DOIUrl":"https://doi.org/10.2478/bile-2022-0006","url":null,"abstract":"Summary The target of this paper is to offer a compact review of the so called distance methods in Statistics, which cover all the known estimation methods. Based on this fact we propose a new step, to adopt from Information Theory, the divergence measures, as distance methods, to compare two distributions, and not only to investigate if the means or the variances of the distributions are equal. Some useful results towards this line of thought are presented, adopting a compact form for all known divergence measures, and are appropriately analyzed for Biometrical, and not only, applications.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77618300","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: 1
Environmental impact on downy mildew infection for different pea varieties 环境对不同豌豆品种霜霉病感染的影响
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0002
E. Bakinowska, W. Pilarczyk, B. Zawieja, A. Szczepańska-Álvarez
{"title":"Environmental impact on downy mildew infection for different pea varieties","authors":"E. Bakinowska, W. Pilarczyk, B. Zawieja, A. Szczepańska-Álvarez","doi":"10.2478/bile-2022-0002","DOIUrl":"https://doi.org/10.2478/bile-2022-0002","url":null,"abstract":"Summary In general, varieties of any cultivated species can differ in many aspects. One of the desirable traits in breeding new varieties is high yield, which can be significantly reduced by plant diseases. This study is an extension of previous research about the resistance of seed pea lines to downy mildew, and provides an extended analysis of this type of experiment. The probability of a degree of infection is determined based on a logistic model with a multinomial distribution. In the analysis the impact of a fixed effect of variety and random environmental effects is considered. It is shown that the environmental effects (combinations of years and location – macro-environments) significantly influence the resistance to diseases, and the differences among environments are larger than the variability of differences among genotypes over all environments. For two types of soils (light and rich) the most resistant varieties, which are significantly different from the control variety, are indicated.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91314383","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: 0
Relative exponential sum-symmetry model and orthogonal decomposition of the sum-symmetry model for ordinal square contingency tables 序方列联表的相对指数和对称模型及和对称模型的正交分解
Biometrical Letters Pub Date : 2022-06-01 DOI: 10.2478/bile-2022-0001
S. Ando
{"title":"Relative exponential sum-symmetry model and orthogonal decomposition of the sum-symmetry model for ordinal square contingency tables","authors":"S. Ando","doi":"10.2478/bile-2022-0001","DOIUrl":"https://doi.org/10.2478/bile-2022-0001","url":null,"abstract":"Summary This study proposes a new exponential sum-symmetry model for square contingency tables with same row and column ordinal classifications. In the existing exponential sum-symmetry (ESS) model, the probability that the sum of row and column levels is t, where the row level is less than the column level, is ∆t−2 times higher than the probability that the sum of row and column levels is t, where the row level is greater than the column level. On the other hand, in the proposed ESS model, the ratio of these two probabilities is ∆t/3. In other words, in the existing ESS model, the ratio of the two probabilities varies exponentially depending on the absolute gap between t and 2, while in the proposed ESS model, the ratio of the two probabilities varies exponentially depending on the relative gap between t and 3, although in both ESS models, the ratio of the two probabilities is ∆ when t is the minimum value (i.e., t = 3). Moreover, this study introduces a new decomposition theorem for the sum-symmetry model using the proposed ESS. The proposed decomposition theorem satisfies asymptotic equivalence for the test statistic.","PeriodicalId":8933,"journal":{"name":"Biometrical Letters","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78185522","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: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信