SlideShare uma empresa Scribd logo

Multivariate data analysis and visualization tools for biological data

•Transferir como PPT, PDF•
•
Dmitry Grapov
Dmitry Grapov
EducaçãoTecnologia
1 de 41
Multivariate Data Analysis and Visualization Tools for Understanding Biological Data Dmitry Grapov
Introduction: Systems Oltvai, et al. Science 25 October 2002: 763-764. Emergent Reductionist Deterministic Systems Complex systems Chemical analysis Physiology Biochemistry Graph theory Modeling Informatics
Introduction: Inference
http://www.thefullwiki.org/Hypercube Overview many correlation mean Central Idea: dendrograms heatmaps biplots networks scatter plots histograms densities Representations: matrix matrix vector Properties: Multivariate n-D Bivariate 2-D Univariate 1-D Types:
Univariate: Properties ,[object Object],[object Object],[object Object]
Univariate: Representations
Univariate: Assumptions ,[object Object]
Univariate: Utility ,[object Object],[object Object],[object Object],[object Object],[object Object]
Univariate: Limitations ,[object Object],[object Object],[object Object],[object Object]
Old Faithful Data ,[object Object],[object Object],[object Object],[object Object],[object Object],Azzalini, A. and Bowman, A. W. (1990). A look at some data on the Old Faithful geyser. Applied Statistics 39 , 357–365
[object Object],Bivariate: Properties
( X , Y ) Bivariate: Representations
( X , Y ) Bivariate: Utility ,[object Object],[object Object],Variable 2 = m* Variable 1 + b
http://en.wikipedia.org/wiki/Correlation Bivariate: Limitations correlation coefficient ,[object Object]
http://en.wikipedia.org/wiki/Correlation Bivariate: Limitations ,[object Object]
Old Faithful Azzalini, A. and Bowman, A. W. (1990). A look at some data on the Old Faithful geyser. Applied Statistics 39 , 357–365
Old Unfaithful?
Old Unfaithful? ,[object Object],[object Object],[object Object]
Old Unfaithful? ,[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],A matrix of n vectors of length m Multivariate: Properties Correlation matrix
[object Object],[object Object],[object Object],[object Object],[object Object],Multivariate: Dimensional Reduction PC 2 PC 1
Multivariate: Dimensional Reduction Wall, Michael E., Andreas Rechtsteiner, Luis M. Rocha."Singular value decomposition and principal component analysis". in  A Practical Approach to Microarray Data Analysis . D.P. Berrar, W. Dubitzky, M. Granzow, eds. pp. 91-109, Kluwer: Norwell, MA (2003). LANL LA-UR-02-4001. Scores Loadings Explained variance m x PC PC x PC n x PC Original Data Calculating PCs: singular value decomposition (SVD) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],A matrix of n vectors of length m Multivariate: Representations
Multivariate: Representation Identify outliers using all measurements Use known to impute missing Identify interesting groups Evaluate uni- and bivariate observations ,[object Object]
PCA: Considerations ,[object Object],[object Object],[object Object],[object Object],no pre-treatment centered and scaled to unit variance
PCA: Considerations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Use ICA to calculate statistically independent components
PCA: Considerations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],NMF uses additive parts based encoding Learning the parts of objects by nonnegative matrix factorization, D.D. Lee,H.S. Seung, Zhipeng Zhao, ppt.
PCA: Considerations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
PLS/-DA: Utility ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
PLS-DA: Example ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Select the appropriate number Latent Variables (LVs) to maximize Q2
PLS-DA: Performance ,[object Object]
PLS-DA: Performance ,[object Object]
PLS: Predictive Performance ,[object Object],[object Object],[object Object]
PLS: Predictive Performance
PLS: Feature Selection Use the PLS-DA as an objective function to identify the most informative variables
Networks ,[object Object],[object Object],[object Object],[object Object],[object Object]
Networks ,[object Object]
Networks ,[object Object],non-diabetics type 2 diabetics
Networks ,[object Object],non-diabetics type 2 diabetics
non-diabetics type 2 diabetics imDEV : interactive modules for Data Exploration and Visualization   An integrated environment for systems level analysis of multivariate data. http:// sourceforge.net/apps/mediawiki/imdev
Acknowledgements Newman Lab Designated Emphasis in Biotechnology (DEB) NIH This project is funded in part by the NIH grant NIGMS-NIH T32-GM008799, USDA-ARS 5306-51530-019-00D, and NIH-NIDDK R01DK078328 -01.

Recomendados

Drug release in Tissue engineering
Drug release in Tissue engineering Drug release in Tissue engineering
Drug release in Tissue engineering Ahmed Ali
 
Software Development Techniques
Software Development TechniquesSoftware Development Techniques
Software Development TechniquesWe Learn - A Continuous Learning Forum from Welingkar's Distance Learning Program.
 
Software Development Methodologies
Software Development MethodologiesSoftware Development Methodologies
Software Development MethodologiesNicholas Davis
 
Ch 6
Ch 6Ch 6
Ch 6Mohammed Romi
 
General principles of tissue organization
General principles of tissue organizationGeneral principles of tissue organization
General principles of tissue organizationEneutron
 
Storm Prediction data analysis using R/SAS
Storm Prediction data analysis using R/SASStorm Prediction data analysis using R/SAS
Storm Prediction data analysis using R/SASGautam Sawant
 
Ch 5- Achieving Qualities
Ch 5- Achieving QualitiesCh 5- Achieving Qualities
Ch 5- Achieving QualitiesAsmat Zahra
 
Regression analysis
Regression analysisRegression analysis
Regression analysisSubin Raj
 

Recomendados

Drug release in Tissue engineering
Drug release in Tissue engineering Drug release in Tissue engineering
Drug release in Tissue engineering Ahmed Ali
 
Software Development Techniques
Software Development TechniquesSoftware Development Techniques
Software Development TechniquesWe Learn - A Continuous Learning Forum from Welingkar's Distance Learning Program.
 
Software Development Methodologies
Software Development MethodologiesSoftware Development Methodologies
Software Development MethodologiesNicholas Davis
 
Ch 6
Ch 6Ch 6
Ch 6Mohammed Romi
 
General principles of tissue organization
General principles of tissue organizationGeneral principles of tissue organization
General principles of tissue organizationEneutron
 
Storm Prediction data analysis using R/SAS
Storm Prediction data analysis using R/SASStorm Prediction data analysis using R/SAS
Storm Prediction data analysis using R/SASGautam Sawant
 
Ch 5- Achieving Qualities
Ch 5- Achieving QualitiesCh 5- Achieving Qualities
Ch 5- Achieving QualitiesAsmat Zahra
 
Regression analysis
Regression analysisRegression analysis
Regression analysisSubin Raj
 
Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.drucsamal
 
Regression
RegressionRegression
Regressionmandrewmartin
 
Linear models
Linear modelsLinear models
Linear modelsFAO
 
Please Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the DeadPlease Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the DeadChristian Crumlish
 
Solving stepwise regression problems
Solving stepwise regression problemsSolving stepwise regression problems
Solving stepwise regression problemsSoma Sinha Roy
 
Architectural structures and views
Architectural structures and viewsArchitectural structures and views
Architectural structures and viewsDr Reeja S R
 
Software Myths
Software MythsSoftware Myths
Software MythsRajat Bajaj
 
software engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semestersoftware engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semesterrajesh199155
 
4 partial least squares modeling
4 partial least squares modeling4 partial least squares modeling
4 partial least squares modelingDmitry Grapov
 
Multivariate data analysis
Multivariate data analysisMultivariate data analysis
Multivariate data analysisSetia Pramana
 
Multivariate Data Visualization
Multivariate Data VisualizationMultivariate Data Visualization
Multivariate Data Visualizationanilash
 
Ecology jt2012
Ecology jt2012Ecology jt2012
Ecology jt2012Caroline Holmes
 
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1Droit ZeitGeist
 
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015Till Rohrmann
 
Multivariate statistics
Multivariate statisticsMultivariate statistics
Multivariate statisticsVeneficus
 
Multivariate
MultivariateMultivariate
Multivariatedessybudiyanti
 
Connecting Metabolomic Data with Context
Connecting Metabolomic Data with ContextConnecting Metabolomic Data with Context
Connecting Metabolomic Data with ContextDmitry Grapov
 
Complex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine LearningComplex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine LearningDmitry Grapov
 
High Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and VisualizationHigh Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and VisualizationDmitry Grapov
 
Automation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report GenerationAutomation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report GenerationDmitry Grapov
 
Mapping to the Metabolomic Manifold
Mapping to the Metabolomic ManifoldMapping to the Metabolomic Manifold
Mapping to the Metabolomic ManifoldDmitry Grapov
 
Theories Of Normality
Theories Of NormalityTheories Of Normality
Theories Of NormalityJade Sun
 

Mais conteúdo relacionado

Mais procurados

Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.drucsamal
 
Linear models
Linear modelsLinear models
Linear modelsFAO
 
Please Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the DeadPlease Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the DeadChristian Crumlish
 
Solving stepwise regression problems
Solving stepwise regression problemsSolving stepwise regression problems
Solving stepwise regression problemsSoma Sinha Roy
 
Architectural structures and views
Architectural structures and viewsArchitectural structures and views
Architectural structures and viewsDr Reeja S R
 
software engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semestersoftware engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semesterrajesh199155
 

Mais procurados (8)

Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.Tissue engineering in heart and valve failure management.
Tissue engineering in heart and valve failure management.
 
Regression
RegressionRegression
Regression
 
Linear models
Linear modelsLinear models
Linear models
 
Please Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the DeadPlease Forget You Knew My Name: Secretly Influenced by the Dead
Please Forget You Knew My Name: Secretly Influenced by the Dead
 
Solving stepwise regression problems
Solving stepwise regression problemsSolving stepwise regression problems
Solving stepwise regression problems
 
Architectural structures and views
Architectural structures and viewsArchitectural structures and views
Architectural structures and views
 
Software Myths
Software MythsSoftware Myths
Software Myths
 
software engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semestersoftware engineering notes for cse/it fifth semester
software engineering notes for cse/it fifth semester
 

Destaque

4 partial least squares modeling
4 partial least squares modeling4 partial least squares modeling
4 partial least squares modelingDmitry Grapov
 
Multivariate data analysis
Multivariate data analysisMultivariate data analysis
Multivariate data analysisSetia Pramana
 
Multivariate Data Visualization
Multivariate Data VisualizationMultivariate Data Visualization
Multivariate Data Visualizationanilash
 
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1Droit ZeitGeist
 
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015Till Rohrmann
 
Multivariate statistics
Multivariate statisticsMultivariate statistics
Multivariate statisticsVeneficus
 
Connecting Metabolomic Data with Context
Connecting Metabolomic Data with ContextConnecting Metabolomic Data with Context
Connecting Metabolomic Data with ContextDmitry Grapov
 
Complex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine LearningComplex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine LearningDmitry Grapov
 
High Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and VisualizationHigh Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and VisualizationDmitry Grapov
 
Automation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report GenerationAutomation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report GenerationDmitry Grapov
 
Mapping to the Metabolomic Manifold
Mapping to the Metabolomic ManifoldMapping to the Metabolomic Manifold
Mapping to the Metabolomic ManifoldDmitry Grapov
 
Theories Of Normality
Theories Of NormalityTheories Of Normality
Theories Of NormalityJade Sun
 
Open Universiteit Pls Prestation November 1st
Open Universiteit Pls Prestation November 1stOpen Universiteit Pls Prestation November 1st
Open Universiteit Pls Prestation November 1stPaulGhijsen
 
Human population Ecology
Human population EcologyHuman population Ecology
Human population EcologyMaria Donohue
 
How to write up and report PLS analyses-三星統計張偉豪-20141004
How to write up and report PLS analyses-三星統計張偉豪-20141004How to write up and report PLS analyses-三星統計張偉豪-20141004
How to write up and report PLS analyses-三星統計張偉豪-20141004Beckett Hsieh
 
Gene Ontology Enrichment Network Analysis -Tutorial
Gene Ontology Enrichment Network Analysis -TutorialGene Ontology Enrichment Network Analysis -Tutorial
Gene Ontology Enrichment Network Analysis -TutorialDmitry Grapov
 

Destaque (20)

4 partial least squares modeling
4 partial least squares modeling4 partial least squares modeling
4 partial least squares modeling
 
Multivariate data analysis
Multivariate data analysisMultivariate data analysis
Multivariate data analysis
 
Multivariate Data Visualization
Multivariate Data VisualizationMultivariate Data Visualization
Multivariate Data Visualization
 
Ecology jt2012
Ecology jt2012Ecology jt2012
Ecology jt2012
 
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
188904603 apostila-execucao-fiscal-mauro-luis-rocha-lopes-1
 
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
Computing recommendations at extreme scale with Apache Flink @Buzzwords 2015
 
Multivariate statistics
Multivariate statisticsMultivariate statistics
Multivariate statistics
 
Multivariate
MultivariateMultivariate
Multivariate
 
Connecting Metabolomic Data with Context
Connecting Metabolomic Data with ContextConnecting Metabolomic Data with Context
Connecting Metabolomic Data with Context
 
Complex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine LearningComplex Systems Biology Informed Data Analysis and Machine Learning
Complex Systems Biology Informed Data Analysis and Machine Learning
 
High Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and VisualizationHigh Dimensional Biological Data Analysis and Visualization
High Dimensional Biological Data Analysis and Visualization
 
Automation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report GenerationAutomation of (Biological) Data Analysis and Report Generation
Automation of (Biological) Data Analysis and Report Generation
 
Mapping to the Metabolomic Manifold
Mapping to the Metabolomic ManifoldMapping to the Metabolomic Manifold
Mapping to the Metabolomic Manifold
 
Theories Of Normality
Theories Of NormalityTheories Of Normality
Theories Of Normality
 
Open Universiteit Pls Prestation November 1st
Open Universiteit Pls Prestation November 1stOpen Universiteit Pls Prestation November 1st
Open Universiteit Pls Prestation November 1st
 
An introduction to denial of service attack
An introduction to denial of service attackAn introduction to denial of service attack
An introduction to denial of service attack
 
dos attacks
dos attacksdos attacks
dos attacks
 
Human population Ecology
Human population EcologyHuman population Ecology
Human population Ecology
 
How to write up and report PLS analyses-三星統計張偉豪-20141004
How to write up and report PLS analyses-三星統計張偉豪-20141004How to write up and report PLS analyses-三星統計張偉豪-20141004
How to write up and report PLS analyses-三星統計張偉豪-20141004
 
Gene Ontology Enrichment Network Analysis -Tutorial
Gene Ontology Enrichment Network Analysis -TutorialGene Ontology Enrichment Network Analysis -Tutorial
Gene Ontology Enrichment Network Analysis -Tutorial
 

Semelhante a Multivariate data analysis and visualization tools for biological data

Prote-OMIC Data Analysis and Visualization
Prote-OMIC Data Analysis and VisualizationProte-OMIC Data Analysis and Visualization
Prote-OMIC Data Analysis and VisualizationDmitry Grapov
 
Prediction Of Bioactivity From Chemical Structure
Prediction Of Bioactivity From Chemical StructurePrediction Of Bioactivity From Chemical Structure
Prediction Of Bioactivity From Chemical StructureJeremy Besnard
 
Graphical Structure Learning accelerated with POWER9
Graphical Structure Learning accelerated with POWER9Graphical Structure Learning accelerated with POWER9
Graphical Structure Learning accelerated with POWER9Ganesan Narayanasamy
 
Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
 
CBM Fault Detection by Carl Byington
CBM Fault Detection by Carl ByingtonCBM Fault Detection by Carl Byington
CBM Fault Detection by Carl ByingtonCarl Byington
 
Bayesian statistics
Bayesian statisticsBayesian statistics
Bayesian statisticsSagar Kamble
 
CSCI 6505 Machine Learning Project
CSCI 6505 Machine Learning ProjectCSCI 6505 Machine Learning Project
CSCI 6505 Machine Learning Projectbutest
 
OVium Bioinformatic Solutions
OVium Bioinformatic SolutionsOVium Bioinformatic Solutions
OVium Bioinformatic SolutionsOVium Solutions
 
32_Nov07_MachineLear..
32_Nov07_MachineLear..32_Nov07_MachineLear..
32_Nov07_MachineLear..butest
 
Intro to Model Selection
Intro to Model SelectionIntro to Model Selection
Intro to Model Selectionchenhm
 
20131019 生物物理若手 Journal Club
20131019 生物物理若手 Journal Club20131019 生物物理若手 Journal Club
20131019 生物物理若手 Journal ClubMed_KU
 
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...IIRindia
 
Developmental Mega Sample: Exploring Inter-Individual Variation
Developmental Mega Sample: Exploring Inter-Individual VariationDevelopmental Mega Sample: Exploring Inter-Individual Variation
Developmental Mega Sample: Exploring Inter-Individual VariationSaigeRutherford
 
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...Arinze Akutekwe
 
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...IJCI JOURNAL
 
BPSO&1-NN algorithm-based variable selection for power system stability ident...
BPSO&1-NN algorithm-based variable selection for power system stability ident...BPSO&1-NN algorithm-based variable selection for power system stability ident...
BPSO&1-NN algorithm-based variable selection for power system stability ident...IJAEMSJORNAL
 
Exploiting technical replicate variance in omics data analysis (RepExplore)
Exploiting technical replicate variance in omics data analysis (RepExplore)Exploiting technical replicate variance in omics data analysis (RepExplore)
Exploiting technical replicate variance in omics data analysis (RepExplore)Enrico Glaab
 
Crystallization classification semisupervised
Crystallization classification semisupervisedCrystallization classification semisupervised
Crystallization classification semisupervisedMadhav Sigdel
 
IRJET- Disease Prediction using Machine Learning
IRJET- Disease Prediction using Machine LearningIRJET- Disease Prediction using Machine Learning
IRJET- Disease Prediction using Machine LearningIRJET Journal
 

Semelhante a Multivariate data analysis and visualization tools for biological data (20)

Prote-OMIC Data Analysis and Visualization
Prote-OMIC Data Analysis and VisualizationProte-OMIC Data Analysis and Visualization
Prote-OMIC Data Analysis and Visualization
 
Prediction Of Bioactivity From Chemical Structure
Prediction Of Bioactivity From Chemical StructurePrediction Of Bioactivity From Chemical Structure
Prediction Of Bioactivity From Chemical Structure
 
Graphical Structure Learning accelerated with POWER9
Graphical Structure Learning accelerated with POWER9Graphical Structure Learning accelerated with POWER9
Graphical Structure Learning accelerated with POWER9
 
Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)
 
Basen Network
Basen NetworkBasen Network
Basen Network
 
CBM Fault Detection by Carl Byington
CBM Fault Detection by Carl ByingtonCBM Fault Detection by Carl Byington
CBM Fault Detection by Carl Byington
 
Bayesian statistics
Bayesian statisticsBayesian statistics
Bayesian statistics
 
CSCI 6505 Machine Learning Project
CSCI 6505 Machine Learning ProjectCSCI 6505 Machine Learning Project
CSCI 6505 Machine Learning Project
 
OVium Bioinformatic Solutions
OVium Bioinformatic SolutionsOVium Bioinformatic Solutions
OVium Bioinformatic Solutions
 
32_Nov07_MachineLear..
32_Nov07_MachineLear..32_Nov07_MachineLear..
32_Nov07_MachineLear..
 
Intro to Model Selection
Intro to Model SelectionIntro to Model Selection
Intro to Model Selection
 
20131019 生物物理若手 Journal Club
20131019 生物物理若手 Journal Club20131019 生物物理若手 Journal Club
20131019 生物物理若手 Journal Club
 
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...
Comparative Analysis of Weighted Emphirical Optimization Algorithm and Lazy C...
 
Developmental Mega Sample: Exploring Inter-Individual Variation
Developmental Mega Sample: Exploring Inter-Individual VariationDevelopmental Mega Sample: Exploring Inter-Individual Variation
Developmental Mega Sample: Exploring Inter-Individual Variation
 
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...
Inference of Nonlinear Gene Regulatory Networks through Optimized Ensemble of...
 
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...
POSTERIOR RESOLUTION AND STRUCTURAL MODIFICATION FOR PARAMETER DETERMINATION ...
 
BPSO&1-NN algorithm-based variable selection for power system stability ident...
BPSO&1-NN algorithm-based variable selection for power system stability ident...BPSO&1-NN algorithm-based variable selection for power system stability ident...
BPSO&1-NN algorithm-based variable selection for power system stability ident...
 
Exploiting technical replicate variance in omics data analysis (RepExplore)
Exploiting technical replicate variance in omics data analysis (RepExplore)Exploiting technical replicate variance in omics data analysis (RepExplore)
Exploiting technical replicate variance in omics data analysis (RepExplore)
 
Crystallization classification semisupervised
Crystallization classification semisupervisedCrystallization classification semisupervised
Crystallization classification semisupervised
 
IRJET- Disease Prediction using Machine Learning
IRJET- Disease Prediction using Machine LearningIRJET- Disease Prediction using Machine Learning
IRJET- Disease Prediction using Machine Learning
 

Mais de Dmitry Grapov

R programming for Data Science - A Beginner’s Guide
R programming for Data Science - A Beginner’s GuideR programming for Data Science - A Beginner’s Guide
R programming for Data Science - A Beginner’s GuideDmitry Grapov
 
Network mapping 101 course
Network mapping 101 courseNetwork mapping 101 course
Network mapping 101 courseDmitry Grapov
 
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...Dmitry Grapov
 
Dmitry Grapov Resume and CV
Dmitry Grapov Resume and CVDmitry Grapov Resume and CV
Dmitry Grapov Resume and CVDmitry Grapov
 
Machine Learning Powered Metabolomic Network Analysis
Machine Learning Powered Metabolomic Network AnalysisMachine Learning Powered Metabolomic Network Analysis
Machine Learning Powered Metabolomic Network AnalysisDmitry Grapov
 
Data analysis workflows part 1 2015
Data analysis workflows part 1 2015Data analysis workflows part 1 2015
Data analysis workflows part 1 2015Dmitry Grapov
 
Data analysis workflows part 2 2015
Data analysis workflows part 2 2015Data analysis workflows part 2 2015
Data analysis workflows part 2 2015Dmitry Grapov
 
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses Dmitry Grapov
 
Case Study: Overview of Metabolomic Data Normalization Strategies
Case Study: Overview of Metabolomic Data Normalization StrategiesCase Study: Overview of Metabolomic Data Normalization Strategies
Case Study: Overview of Metabolomic Data Normalization StrategiesDmitry Grapov
 
3 data normalization (2014 lab tutorial)
3 data normalization (2014 lab tutorial)3 data normalization (2014 lab tutorial)
3 data normalization (2014 lab tutorial)Dmitry Grapov
 
Normalization of Large-Scale Metabolomic Studies 2014
Normalization of Large-Scale Metabolomic Studies 2014Normalization of Large-Scale Metabolomic Studies 2014
Normalization of Large-Scale Metabolomic Studies 2014Dmitry Grapov
 
American Society of Mass Spectrommetry Conference 2014
American Society of Mass Spectrommetry Conference 2014American Society of Mass Spectrommetry Conference 2014
American Society of Mass Spectrommetry Conference 2014Dmitry Grapov
 
Multivarite and network tools for biological data analysis
Multivarite and network tools for biological data analysisMultivarite and network tools for biological data analysis
Multivarite and network tools for biological data analysisDmitry Grapov
 
Data Normalization Approaches for Large-scale Biological Studies
Data Normalization Approaches for Large-scale Biological StudiesData Normalization Approaches for Large-scale Biological Studies
Data Normalization Approaches for Large-scale Biological StudiesDmitry Grapov
 
Omic Data Integration Strategies
Omic Data Integration StrategiesOmic Data Integration Strategies
Omic Data Integration StrategiesDmitry Grapov
 
Metabolomic data analysis and visualization tools
Metabolomic data analysis and visualization toolsMetabolomic data analysis and visualization tools
Metabolomic data analysis and visualization toolsDmitry Grapov
 
6 metabolite enrichment analysis
6 metabolite enrichment analysis6 metabolite enrichment analysis
6 metabolite enrichment analysisDmitry Grapov
 
5 data analysis case study
5 data analysis case study5 data analysis case study
5 data analysis case studyDmitry Grapov
 
3 principal components analysis
3 principal components analysis3 principal components analysis
3 principal components analysisDmitry Grapov
 

Mais de Dmitry Grapov (20)

R programming for Data Science - A Beginner’s Guide
R programming for Data Science - A Beginner’s GuideR programming for Data Science - A Beginner’s Guide
R programming for Data Science - A Beginner’s Guide
 
Network mapping 101 course
Network mapping 101 courseNetwork mapping 101 course
Network mapping 101 course
 
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...
 
Dmitry Grapov Resume and CV
Dmitry Grapov Resume and CVDmitry Grapov Resume and CV
Dmitry Grapov Resume and CV
 
Machine Learning Powered Metabolomic Network Analysis
Machine Learning Powered Metabolomic Network AnalysisMachine Learning Powered Metabolomic Network Analysis
Machine Learning Powered Metabolomic Network Analysis
 
Data analysis workflows part 1 2015
Data analysis workflows part 1 2015Data analysis workflows part 1 2015
Data analysis workflows part 1 2015
 
Data analysis workflows part 2 2015
Data analysis workflows part 2 2015Data analysis workflows part 2 2015
Data analysis workflows part 2 2015
 
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses
Metabolomics and Beyond Challenges and Strategies for Next-gen Omic Analyses
 
Case Study: Overview of Metabolomic Data Normalization Strategies
Case Study: Overview of Metabolomic Data Normalization StrategiesCase Study: Overview of Metabolomic Data Normalization Strategies
Case Study: Overview of Metabolomic Data Normalization Strategies
 
Modeling poster
Modeling posterModeling poster
Modeling poster
 
3 data normalization (2014 lab tutorial)
3 data normalization (2014 lab tutorial)3 data normalization (2014 lab tutorial)
3 data normalization (2014 lab tutorial)
 
Normalization of Large-Scale Metabolomic Studies 2014
Normalization of Large-Scale Metabolomic Studies 2014Normalization of Large-Scale Metabolomic Studies 2014
Normalization of Large-Scale Metabolomic Studies 2014
 
American Society of Mass Spectrommetry Conference 2014
American Society of Mass Spectrommetry Conference 2014American Society of Mass Spectrommetry Conference 2014
American Society of Mass Spectrommetry Conference 2014
 
Multivarite and network tools for biological data analysis
Multivarite and network tools for biological data analysisMultivarite and network tools for biological data analysis
Multivarite and network tools for biological data analysis
 
Data Normalization Approaches for Large-scale Biological Studies
Data Normalization Approaches for Large-scale Biological StudiesData Normalization Approaches for Large-scale Biological Studies
Data Normalization Approaches for Large-scale Biological Studies
 
Omic Data Integration Strategies
Omic Data Integration StrategiesOmic Data Integration Strategies
Omic Data Integration Strategies
 
Metabolomic data analysis and visualization tools
Metabolomic data analysis and visualization toolsMetabolomic data analysis and visualization tools
Metabolomic data analysis and visualization tools
 
6 metabolite enrichment analysis
6 metabolite enrichment analysis6 metabolite enrichment analysis
6 metabolite enrichment analysis
 
5 data analysis case study
5 data analysis case study5 data analysis case study
5 data analysis case study
 
3 principal components analysis
3 principal components analysis3 principal components analysis
3 principal components analysis
 

Último

Python Notes for mca i year students osmania university.docx
Python Notes for mca i year students osmania university.docxPython Notes for mca i year students osmania university.docx
Python Notes for mca i year students osmania university.docxRamakrishna Reddy Bijjam
 
Measures of Central Tendency: Mean, Median and Mode
Measures of Central Tendency: Mean, Median and ModeMeasures of Central Tendency: Mean, Median and Mode
Measures of Central Tendency: Mean, Median and ModeThiyagu K
 
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhi
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in DelhiRussian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhi
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhikauryashika82
 
Class 11th Physics NEET formula sheet pdf
Class 11th Physics NEET formula sheet pdfClass 11th Physics NEET formula sheet pdf
Class 11th Physics NEET formula sheet pdfAyushMahapatra5
 
ICT role in 21st century education and it's challenges.
ICT role in 21st century education and it's challenges.ICT role in 21st century education and it's challenges.
ICT role in 21st century education and it's challenges.MaryamAhmad92
 
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesMixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesCeline George
 
Measures of Dispersion and Variability: Range, QD, AD and SD
Measures of Dispersion and Variability: Range, QD, AD and SDMeasures of Dispersion and Variability: Range, QD, AD and SD
Measures of Dispersion and Variability: Range, QD, AD and SDThiyagu K
 
Activity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfActivity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfciinovamais
 
psychiatric nursing HISTORY COLLECTION .docx
psychiatric nursing HISTORY COLLECTION .docxpsychiatric nursing HISTORY COLLECTION .docx
psychiatric nursing HISTORY COLLECTION .docxPoojaSen20
 
Sociology 101 Demonstration of Learning Exhibit
Sociology 101 Demonstration of Learning ExhibitSociology 101 Demonstration of Learning Exhibit
Sociology 101 Demonstration of Learning Exhibitjbellavia9
 
General Principles of Intellectual Property: Concepts of Intellectual Proper...
General Principles of Intellectual Property: Concepts of Intellectual Proper...General Principles of Intellectual Property: Concepts of Intellectual Proper...
General Principles of Intellectual Property: Concepts of Intellectual Proper...Poonam Aher Patil
 
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-II
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-IIFood Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-II
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-IIShubhangi Sonawane
 
This PowerPoint helps students to consider the concept of infinity.
This PowerPoint helps students to consider the concept of infinity.This PowerPoint helps students to consider the concept of infinity.
This PowerPoint helps students to consider the concept of infinity.christianmathematics
 
Application orientated numerical on hev.ppt
Application orientated numerical on hev.pptApplication orientated numerical on hev.ppt
Application orientated numerical on hev.pptRamjanShidvankar
 
1029 - Danh muc Sach Giao Khoa 10 . pdf
1029 - Danh muc Sach Giao Khoa 10 . pdf1029 - Danh muc Sach Giao Khoa 10 . pdf
1029 - Danh muc Sach Giao Khoa 10 . pdfQucHHunhnh
 
On National Teacher Day, meet the 2024-25 Kenan Fellows
On National Teacher Day, meet the 2024-25 Kenan FellowsOn National Teacher Day, meet the 2024-25 Kenan Fellows
On National Teacher Day, meet the 2024-25 Kenan FellowsMebane Rash
 
Making and Justifying Mathematical Decisions.pdf
Making and Justifying Mathematical Decisions.pdfMaking and Justifying Mathematical Decisions.pdf
Making and Justifying Mathematical Decisions.pdfChris Hunter
 
Beyond the EU: DORA and NIS 2 Directive's Global Impact
Beyond the EU: DORA and NIS 2 Directive's Global ImpactBeyond the EU: DORA and NIS 2 Directive's Global Impact
Beyond the EU: DORA and NIS 2 Directive's Global ImpactPECB
 

Último (20)

Python Notes for mca i year students osmania university.docx
Python Notes for mca i year students osmania university.docxPython Notes for mca i year students osmania university.docx
Python Notes for mca i year students osmania university.docx
 
Measures of Central Tendency: Mean, Median and Mode
Measures of Central Tendency: Mean, Median and ModeMeasures of Central Tendency: Mean, Median and Mode
Measures of Central Tendency: Mean, Median and Mode
 
Mehran University Newsletter Vol-X, Issue-I, 2024
Mehran University Newsletter Vol-X, Issue-I, 2024Mehran University Newsletter Vol-X, Issue-I, 2024
Mehran University Newsletter Vol-X, Issue-I, 2024
 
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhi
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in DelhiRussian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhi
Russian Escort Service in Delhi 11k Hotel Foreigner Russian Call Girls in Delhi
 
Asian American Pacific Islander Month DDSD 2024.pptx
Asian American Pacific Islander Month DDSD 2024.pptxAsian American Pacific Islander Month DDSD 2024.pptx
Asian American Pacific Islander Month DDSD 2024.pptx
 
Class 11th Physics NEET formula sheet pdf
Class 11th Physics NEET formula sheet pdfClass 11th Physics NEET formula sheet pdf
Class 11th Physics NEET formula sheet pdf
 
ICT role in 21st century education and it's challenges.
ICT role in 21st century education and it's challenges.ICT role in 21st century education and it's challenges.
ICT role in 21st century education and it's challenges.
 
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin ClassesMixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
Mixin Classes in Odoo 17 How to Extend Models Using Mixin Classes
 
Measures of Dispersion and Variability: Range, QD, AD and SD
Measures of Dispersion and Variability: Range, QD, AD and SDMeasures of Dispersion and Variability: Range, QD, AD and SD
Measures of Dispersion and Variability: Range, QD, AD and SD
 
Activity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdfActivity 01 - Artificial Culture (1).pdf
Activity 01 - Artificial Culture (1).pdf
 
psychiatric nursing HISTORY COLLECTION .docx
psychiatric nursing HISTORY COLLECTION .docxpsychiatric nursing HISTORY COLLECTION .docx
psychiatric nursing HISTORY COLLECTION .docx
 
Sociology 101 Demonstration of Learning Exhibit
Sociology 101 Demonstration of Learning ExhibitSociology 101 Demonstration of Learning Exhibit
Sociology 101 Demonstration of Learning Exhibit
 
General Principles of Intellectual Property: Concepts of Intellectual Proper...
General Principles of Intellectual Property: Concepts of Intellectual Proper...General Principles of Intellectual Property: Concepts of Intellectual Proper...
General Principles of Intellectual Property: Concepts of Intellectual Proper...
 
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-II
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-IIFood Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-II
Food Chain and Food Web (Ecosystem) EVS, B. Pharmacy 1st Year, Sem-II
 
This PowerPoint helps students to consider the concept of infinity.
This PowerPoint helps students to consider the concept of infinity.This PowerPoint helps students to consider the concept of infinity.
This PowerPoint helps students to consider the concept of infinity.
 
Application orientated numerical on hev.ppt
Application orientated numerical on hev.pptApplication orientated numerical on hev.ppt
Application orientated numerical on hev.ppt
 
1029 - Danh muc Sach Giao Khoa 10 . pdf
1029 - Danh muc Sach Giao Khoa 10 . pdf1029 - Danh muc Sach Giao Khoa 10 . pdf
1029 - Danh muc Sach Giao Khoa 10 . pdf
 
On National Teacher Day, meet the 2024-25 Kenan Fellows
On National Teacher Day, meet the 2024-25 Kenan FellowsOn National Teacher Day, meet the 2024-25 Kenan Fellows
On National Teacher Day, meet the 2024-25 Kenan Fellows
 
Making and Justifying Mathematical Decisions.pdf
Making and Justifying Mathematical Decisions.pdfMaking and Justifying Mathematical Decisions.pdf
Making and Justifying Mathematical Decisions.pdf
 
Beyond the EU: DORA and NIS 2 Directive's Global Impact
Beyond the EU: DORA and NIS 2 Directive's Global ImpactBeyond the EU: DORA and NIS 2 Directive's Global Impact
Beyond the EU: DORA and NIS 2 Directive's Global Impact
 

Multivariate data analysis and visualization tools for biological data

  • 1. Multivariate Data Analysis and Visualization Tools for Understanding Biological Data Dmitry Grapov
  • 2. Introduction: Systems Oltvai, et al. Science 25 October 2002: 763-764. Emergent Reductionist Deterministic Systems Complex systems Chemical analysis Physiology Biochemistry Graph theory Modeling Informatics
  • 4. http://www.thefullwiki.org/Hypercube Overview many correlation mean Central Idea: dendrograms heatmaps biplots networks scatter plots histograms densities Representations: matrix matrix vector Properties: Multivariate n-D Bivariate 2-D Univariate 1-D Types:
  • 5.
  • 7.
  • 8.
  • 9.
  • 10.
  • 11.
  • 12. ( X , Y ) Bivariate: Representations
  • 13.
  • 14.
  • 15.
  • 16. Old Faithful Azzalini, A. and Bowman, A. W. (1990). A look at some data on the Old Faithful geyser. Applied Statistics 39 , 357–365
  • 18.
  • 19.
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.
  • 25.
  • 26.
  • 27.
  • 28.
  • 29.
  • 30.
  • 31.
  • 32.
  • 33.
  • 35. PLS: Feature Selection Use the PLS-DA as an objective function to identify the most informative variables
  • 36.
  • 37.
  • 38.
  • 39.
  • 40. non-diabetics type 2 diabetics imDEV : interactive modules for Data Exploration and Visualization   An integrated environment for systems level analysis of multivariate data. http:// sourceforge.net/apps/mediawiki/imdev
  • 41. Acknowledgements Newman Lab Designated Emphasis in Biotechnology (DEB) NIH This project is funded in part by the NIH grant NIGMS-NIH T32-GM008799, USDA-ARS 5306-51530-019-00D, and NIH-NIDDK R01DK078328 -01.