Strategies for Metabolomics Data AnalysisDmitry Grapov
Part of a lectures series for the international summer course in metabolomics 2013 (http://metabolomics.ucdavis.edu/courses-and-seminars/courses). Get more material and information here (http://imdevsoftware.wordpress.com/2013/09/08/sessions-in-metabolomics-2013/).
Case Study: Overview of Metabolomic Data Normalization StrategiesDmitry Grapov
Five normalization methods were compared, of which the combination of qc-LOESS and cubic splines showed the best performance based on within-batch and between-batch variable relative standard deviations for QCs. This approach was used to normalize sample measurements the results of which were analyzed using principal components analysis.
Strategies for Metabolomics Data AnalysisDmitry Grapov
Part of a lectures series for the international summer course in metabolomics 2013 (http://metabolomics.ucdavis.edu/courses-and-seminars/courses). Get more material and information here (http://imdevsoftware.wordpress.com/2013/09/08/sessions-in-metabolomics-2013/).
Case Study: Overview of Metabolomic Data Normalization StrategiesDmitry Grapov
Five normalization methods were compared, of which the combination of qc-LOESS and cubic splines showed the best performance based on within-batch and between-batch variable relative standard deviations for QCs. This approach was used to normalize sample measurements the results of which were analyzed using principal components analysis.
Data Normalization Approaches for Large-scale Biological StudiesDmitry Grapov
Overview of how to estimate data quality and validate normalization approaches to remove analytical variance.
See here for animations used in the presentation:
http://imdevsoftware.wordpress.com/2014/06/04/using-repeated-measures-to-remove-artifacts-from-longitudinal-data/
This presentation describes the concept of One Sample t-test, Independent Sample t-test and Paired Sample t-test. This presentation also deals about the procedure to do the t-test through SPSS.
Advanced strategies for Metabolomics Data AnalysisDmitry Grapov
Part of a lectures series for the international summer course in metabolomics 2013 (http://metabolomics.ucdavis.edu/courses-and-seminars/courses). Get more material and information here (http://imdevsoftware.wordpress.com/2013/09/08/sessions-in-metabolomics-2013/).
A chapter describing the use and application of exploratory factor analysis using principal axis factoring with oblique rotation.
Provides a step by step guide to exploratory factor analysis using SPSS.
Basic Concepts of Non-Parametric Methods ( Statistics )Hasnat Israq
This gives the basic description of Non-Parametric Methods . This is one of the important topic in Statistics and also for Mathematics and for Researchers-Scientists .
Prote-OMIC Data Analysis and VisualizationDmitry Grapov
Introductory lecture to multivariate analysis of proteomic data.
Material from the UC Davis 2014 Proteomics Workshop.
See more at: http://sourceforge.net/projects/teachingdemos/files/2014%20UC%20Davis%20Proteomics%20Workshop/
Analysis of Variance and Repeated Measures DesignJ P Verma
This presentation discusses the basic concept used in analysis of variance and it shows the difference between independent measures ANOVA and Repeated measures ANOVA
Data Normalization Approaches for Large-scale Biological StudiesDmitry Grapov
Overview of how to estimate data quality and validate normalization approaches to remove analytical variance.
See here for animations used in the presentation:
http://imdevsoftware.wordpress.com/2014/06/04/using-repeated-measures-to-remove-artifacts-from-longitudinal-data/
This presentation describes the concept of One Sample t-test, Independent Sample t-test and Paired Sample t-test. This presentation also deals about the procedure to do the t-test through SPSS.
Advanced strategies for Metabolomics Data AnalysisDmitry Grapov
Part of a lectures series for the international summer course in metabolomics 2013 (http://metabolomics.ucdavis.edu/courses-and-seminars/courses). Get more material and information here (http://imdevsoftware.wordpress.com/2013/09/08/sessions-in-metabolomics-2013/).
A chapter describing the use and application of exploratory factor analysis using principal axis factoring with oblique rotation.
Provides a step by step guide to exploratory factor analysis using SPSS.
Basic Concepts of Non-Parametric Methods ( Statistics )Hasnat Israq
This gives the basic description of Non-Parametric Methods . This is one of the important topic in Statistics and also for Mathematics and for Researchers-Scientists .
Prote-OMIC Data Analysis and VisualizationDmitry Grapov
Introductory lecture to multivariate analysis of proteomic data.
Material from the UC Davis 2014 Proteomics Workshop.
See more at: http://sourceforge.net/projects/teachingdemos/files/2014%20UC%20Davis%20Proteomics%20Workshop/
Analysis of Variance and Repeated Measures DesignJ P Verma
This presentation discusses the basic concept used in analysis of variance and it shows the difference between independent measures ANOVA and Repeated measures ANOVA
Tales of correlation inflation (2013 CADD GRC) Peter Kenny
Presented at 2013 Computer-Aided Drug Design Gordon conference and subtitled, 'Eu prefiro a minha comida cozida e meus dados brutos' and the chicken in the title slide photo had been walking around the day before the photo was taken.
The use of data and its modelling in science provides meaningful interpretation of real world problems. This presentation provides an easy to understand overview of data visualization and analytics , and snippets of data science applications using R - programming.
Sampling based approximation of confidence intervals for functions of genetic...prettygully
Approximate lower bound sampling errors of maximum likelihood estimates of covariance components and their linear functions can be obtained from the inverse of the
information matrix. For non-linear functions, sampling variances are commonly determined as the variance of their first order Taylor series expansions. This is used to obtain sampling errors for estimates of heritabilities and correlations, and these quantities can be computed
with most software performing such analyses. In other instances, however, more complicated functions are of interest or the linear approximation is difficult or inadequate. A pragmatic alternative then is to evaluate sampling characteristics by repeated sampling of parameters from their asymptotic, multivariate normal distribution, calculating the function(s) of interest for each sample and inspecting the distribution across replicates. This paper demonstrates the use of this approach and examines the quality of
approximation obtained.
Similar to Intermediate Strategies for Metabolomic Data Analysis (20)
Full course: https://creativedatasolutions.github.io/CDS.courses/courses/network_mapping_101/docs/
The course covered all of the steps required to go from `raw data` to a rich `mapped biochemical network` incorporating statistical, multivariate and machine learning results. This included [examples](https://creativedatasolutions.github.io/CDS.courses/courses/network_mapping_101/docs/#topics) and tutorials for:
* Preparing raw data for analysis
* Multivariate data exploration
* Supervised clustering
* Machine learning – classification model validation and feature selection
* Network analysis - biochemical, structural similarity and correlation networks
* Network mapping – putting it all together to create a publication quality network
url:
https://github.com/CreativeDataSolutions/CDS.courses/blob/gh-pages/courses/network_mapping_101/materials/lectures/tutorial.pdf
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integratio...Dmitry Grapov
Machine learning (ML) is being ubiquitously incorporated into everyday products such as Internet search, email spam filters, product recommendations, image classification, and speech recognition. New approaches for highly integrated manufacturing and automation such as the Industry 4.0 and the Internet of things are also converging with ML methodologies. Many approaches incorporate complex artificial neural network architectures and are collectively referred to as deep learning (DL) applications. These methods have been shown capable of representing and learning predictable relationships in many diverse forms of data and hold promise for transforming the future of omics research and applications in precision medicine. Omics and electronic health record data pose considerable challenges for DL. This is due to many factors such as low signal to noise, analytical variance, and complex data integration requirements. However, DL models have already been shown capable of both improving the ease of data encoding and predictive model performance over alternative approaches. It may not be surprising that concepts encountered in DL share similarities with those observed in biological message relay systems such as gene, protein, and metabolite networks. This expert review examines the challenges and opportunities for DL at a systems and biological scale for a precision medicine readership.
current: https://drive.google.com/open?id=0B51AEMfo-fh9M3FmWXVlb05pdm8
I am always looking for the next data science, machine learning and visualization challenge.
Here is a link to my up to date
resume:
https://drive.google.com/open?id=0B51AEMfo-fh9M3FmWXVlb05pdm8
cv:
https://drive.google.com/open?id=0B51AEMfo-fh9Z05aM2p6XzFIOFE
https://www.youtube.com/watch?v=Y_-o-4rKxUk
Machine learning powered metabolomic network analysis
Dmitry Grapov PhD,
Director of Data Science and Bioinformatics,
CDS- Creative Data Solutions
www.createdatasol.com
Metabolomic network analysis can be used to interpret experimental results within a variety of contexts including: biochemical relationships, structural and spectral similarity and empirical correlation. Machine learning is useful for modeling relationships in the context of pattern recognition, clustering, classification and regression based predictive modeling. The combination of developed metabolomic networks and machine learning based predictive models offer a unique method to visualize empirical relationships while testing key experimental hypotheses. The following presentation focuses on data analysis, visualization, machine learning and network mapping approaches used to create richly mapped metabolomic networks. Learn more at www.createdatasol.com
3 data normalization (2014 lab tutorial)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also plan to release videos for all the lectures and labs.
Step by step tutorial for conducting GO enrichment analysis and then creating a network from the results.
Material from the UC Davis 2014 Proteomics Workshop.
See more at: http://sourceforge.net/projects/teachingdemos/files/2014%20UC%20Davis%20Proteomics%20Workshop/
Automation of (Biological) Data Analysis and Report GenerationDmitry Grapov
I've been experimenting with automating simple and complex data analysis and report generation tasks for biological data and mostly using R and LATEX. You can see some of my progress and challenges encountered.
Metabolomic data analysis and visualization toolsDmitry Grapov
A description of data analysis and visualization tools for metabolomic and other high dimensional data sets, developed at the NIH West Coast Metabolomics Center.
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
11. Missing Values Imputation
Why is it missing?
•random
•systematic
• analytical
• biological
Imputation methods
•single value (mean, min, etc.)
•multiple
•multivariate
mean
PCA
12. Goals for Data Analysis
• Are there any trends in my data?
– analytical sources
– meta data/covariates
• Useful Methods
– matrix decomposition (PCA, ICA, NMF)
– cluster analysis
• Differences/similarities between groups?
– discrimination, classification, significant changes
• Useful Methods
– analysis of variance (ANOVA)
– partial least squares discriminant analysis (PLS-DA)
– Others: random forest, CART, SVM, ANN
• What is related or predictive of my variable(s) of interest?
– regression
• Useful Methods
Exploration Classification Prediction
13. Data Structure
•univariate: a single variable (1-D)
•bivariate: two variables (2-D)
•multivariate: 2 > variables (m-D)
•Data Types
•continuous
•discreet
• binary
14. Data Complexity
n
m
1-D 2-D m-D
Data
samples
variables
complexity
Meta
Data
Experimental
Design =
Variable # = dimensionality
16. Univariate Analyses
•sensitive to distribution shape
•parametric = assumes normality
•error in Y, not in X (Y = mX + error)
•optimal for long data
•assumed independence
•false discovery rate
long
wide
n-of-one
17. False Discovery Rate (FDR)
univariate approaches do not scale well
• Type I Error: False Positives
•Type II Error: False Negatives
•Type I risk =
•1-(1-p.value)m
m = number of variables tested
18. FDR correction
Example:
Design: 30 sample, 300 variables
Test: t-test
FDR method: Benjamini and
Hochberg (fdr) correction at q=0.05
Bioinformatics (2008) 24 (12):1461-1462
Results
FDR adjusted p-values (fdr) or estimate of FDR (Fdr, q-value)
19. Achieving “significance” is a function of:
significance level (α) and power (1-β )
effect size (standardized difference in
means)
sample size (n)
23. Bivariate Example
Goal: Don’t miss eruption!
Data
•time between eruptions
– 70 ± 14 min
•duration of eruption
– 3.5 ± 1 min
Azzalini, A. and Bowman, A. W. (1990). A look at some data on the Old Faithful
geyser. Applied Statistics 39, 357–365
Old Faithful, Yellowstone, WY
24. Bivariate Example
Two cluster pattern for
both duration and
frequency
Azzalini, A. and Bowman, A. W. (1990). A look at some data on the Old Faithful geyser. Applied Statistics 39, 357–365
26. Covariates
Trends in data
which mask
primary goals
can be
accounted for
using covariate
adjustment
and
appropriate
modeling
strategies
27. Bivariate Example
Noted deviations from
two cluster pattern can
be explained by
covariate:
Hydrofraking
Covariate adjustment
is an integral aspect of
statistical analyses
(e.g. ANCOVA)
28. Summary
Data exploration and pre-analysis:
•increase robustness of results
•guards against spurious findings
•Can greatly improve primary analyses
Univariate Statistics:
•are useful for identification of statically
significant changes or relationships
•sub-optimal for wide data
•best when combined with advanced
multivariate techniques
29. Resources
Web-based data analysis platforms
•MetaboAnalyst(http://www.metaboanalyst.ca/MetaboAnalyst/faces/Home.jsp)
•MeltDB(https://meltdb.cebitec.uni-bielefeld.de/cgi-bin/login.cgi)
Programming tools
•The R Project for Statistical
Computing(http://www.r-project.org/)
•Bioconductor(http://www.bioconductor.org/ )
GUI tools
•imDEV(http://sourceforge.net/projects/imdev/?source=directory)