Statistical Analysis Principles for Omics Data

2011 ◽  
pp. 113-131 ◽  
Author(s):  
Daniela Dunkler ◽  
Fátima Sánchez-Cabo ◽  
Georg Heinze
Keyword(s):  
Statistical Analysis ◽  
Omics Data

scholarly journals Challenges in biomarker discovery: combining expert insights with statistical analysis of complex omics data

2012 ◽  
Vol 7 (1) ◽  
pp. 37-51 ◽  
Author(s):  
Jason E McDermott ◽  
Jing Wang ◽  
Hugh Mitchell ◽  
Bobbie-Jo Webb-Robertson ◽  
Ryan Hafen ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Biomarker Discovery ◽  
Omics Data

scholarly journals Software for the integration of multi-omics experiments in Bioconductor

2017 ◽  
Author(s):  
Marcel Ramos ◽  
Lucas Schiffer ◽  
Angela Re ◽  
Rimsha Azhar ◽  
Azfar Basunia ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Data Science ◽  
Data Representation ◽  
The Cancer Genome Atlas ◽  
Cancer Tissue ◽  
Omics Data ◽  
Data Types ◽  
Design Data ◽  
High Throughput Data ◽  
Cancer Genome Atlas

ABSTRACTMulti-omics experiments are increasingly commonplace in biomedical research, and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multi-omics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide all of the multiple ‘omics data for each cancer tissue in The Cancer Genome Atlas (TCGA) as ready-to-analyze MultiAssayExperiment objects, and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable and reproducible statistical analysis of multi-omics data and enhances data science applications of multiple omics datasets.

scholarly journals IOAT: an interactive tool for statistical analysis of omics data and clinical data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lanlan Wu ◽  
Fei Liu ◽  
Hongmin Cai
Keyword(s):  
Risk Assessment ◽  
Statistical Analysis ◽  
Clinical Data ◽  
High Throughput Sequencing ◽  
Tumor Staging ◽  
Visual Development ◽  
Complete Analysis ◽  
Precision Oncology ◽  
Omics Data ◽  
Cancer Subtypes

Abstract Background With the development of high-throughput sequencing technology, a huge amount of multi-omics data has been accumulated. Although there are many software tools for statistical analysis and visual development of omics data, these tools are not suitable for private data and non-technical users. Besides, most of these tools have specialized in only one or perhaps a few data typesare, without combining clinical information. What’s more, users could not choose data processing and model selection flexibly when using these tools. Results To help non-technical users to understand and analyze private multi-omics data and ensure data security, we developed an interactive desk tool for statistical analysis and visualization of omics and clinical data (shortly IOAT). Our mainly targets csv format data, and combines clinical data with high-dimensional multi-omics data. It also contains various operations, such as data preprocessing, feature selection, risk assessment, clustering, and survival analysis. By using this tool, users can safely and conveniently try a combination of various methods on their private multi-omics data to find a model suitable for their data, conduct risk assessment and determine their cancer subtypes. At the same time, the tool can also provide them with references to genes that are closely related to tumor staging, facilitating the development of precision oncology. We review IOAT’s main features and demonstrate its analysis capabilities on a lung from TCGA. Conclusions IOAT is a local desktop tool, which provides a set of multi-omics data integration solutions. It can quickly perform a complete analysis of cancer genome data for subtype discovery and biomarker identification without security issues and writing any code. Thus, our tool can enable cancer biologists and biomedicine researchers to analyze their data more easily and safely. IOAT can be downloaded for free from https://github.com/WlSunshine/IOAT-software.

Statistical analysis of classification

1966 ◽  
Vol 24 ◽  
pp. 188-189
Author(s):  
T. J. Deeming
Keyword(s):  
Multivariate Analysis ◽  
Statistical Analysis ◽  
Classification Scheme ◽  
Analytical Procedure ◽  
Narrow Band ◽  
Scientific Research ◽  
Maximum Amount ◽  
Amount Of Information

If we make a set of measurements, such as narrow-band or multicolour photo-electric measurements, which are designed to improve a scheme of classification, and in particular if they are designed to extend the number of dimensions of classification, i.e. the number of classification parameters, then some important problems of analytical procedure arise. First, it is important not to reproduce the errors of the classification scheme which we are trying to improve. Second, when trying to extend the number of dimensions of classification we have little or nothing with which to test the validity of the new parameters.Problems similar to these have occurred in other areas of scientific research (notably psychology and education) and the branch of Statistics called Multivariate Analysis has been developed to deal with them. The techniques of this subject are largely unknown to astronomers, but, if carefully applied, they should at the very least ensure that the astronomer gets the maximum amount of information out of his data and does not waste his time looking for information which is not there. More optimistically, these techniques are potentially capable of indicating the number of classification parameters necessary and giving specific formulas for computing them, as well as pinpointing those particular measurements which are most crucial for determining the classification parameters.

Quantitative parallel EELS spectrum imaging developed as a new tool in AEM

1992 ◽  
Vol 50 (2) ◽  
pp. 1202-1203
Author(s):  
Gianluigi Botton ◽  
Gilles L'espérance
Keyword(s):  
Statistical Analysis ◽  
Spatial Resolution ◽  
Personal Computer ◽  
Systematic Study ◽  
Present Author ◽  
Chemical Elements ◽  
Detection Limits ◽  
Research Groups ◽  
Quantitative Performance ◽  
Spectrum Imaging

As interest for parallel EELS spectrum imaging grows in laboratories equipped with commercial spectrometers, different approaches were used in recent years by a few research groups in the development of the technique of spectrum imaging as reported in the literature. Either by controlling, with a personal computer both the microsope and the spectrometer or using more powerful workstations interfaced to conventional multichannel analysers with commercially available programs to control the microscope and the spectrometer, spectrum images can now be obtained. Work on the limits of the technique, in terms of the quantitative performance was reported, however, by the present author where a systematic study of artifacts detection limits, statistical errors as a function of desired spatial resolution and range of chemical elements to be studied in a map was carried out The aim of the present paper is to show an application of quantitative parallel EELS spectrum imaging where statistical analysis is performed at each pixel and interpretation is carried out using criteria established from the statistical analysis and variations in composition are analyzed with the help of information retreived from t/γ maps so that artifacts are avoided.

Intraindividual Variability in Development Within and Between Individuals

2001 ◽  
Vol 6 (3) ◽  
pp. 187-193 ◽  
Author(s):  
John R. Nesselroade
Keyword(s):  
Statistical Analysis ◽  
Research Design ◽  
Intraindividual Variability ◽  
Factor Analytic

A focus on the study of development and other kinds of changes in the whole individual has been one of the hallmarks of research by Magnusson and his colleagues. A number of different approaches emphasize this individual focus in their respective ways. This presentation focuses on intraindividual variability stemming from Cattell's P-technique factor analytic proposals, making several refinements to make it more tractable from a research design standpoint and more appropriate from a statistical analysis perspective. The associated methods make it possible to study intraindividual variability both within and between individuals. An empirical example is used to illustrate the procedure.

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