Brendel Group Presentation: 17 Oct 2013
•Download as PPTX, PDF•
0 likes•257 views
The document describes a study that analyzed differential gene expression between queen and worker castes of the paper wasp Polistes dominula. 12 samples (6 queens and 6 workers) were collected from different colonies. Initial analysis found thousands of differentially expressed transcripts but permutation testing showed this was likely due to noise. Additional filtering reduced the number of transcripts and samples analyzed. The top differentially expressed transcripts were presented, with one transcript showing a fold change of 126 between castes.
Report
Share
Report
Share
![Experimental design
6 queen samples
6 worker samples
Queen x and worker x from same colony
(x ∈ [1 .. 6])
Hypothesis: identify handful of critical
caste-related genes/transcripts](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
Recommended
DESeq Paper Journal club
DESeq models read counts with a negative binomial distribution to account for biological variability between samples, which a Poisson distribution underestimates. It estimates variance for each gene based on a local regression of variance against mean expression of other genes. This allows it to better control false positives compared to EdgeR or a Poisson model. DESeq also estimates sequencing depth differently than EdgeR to improve differential expression testing across the dynamic range of expression levels.
GSSD13 Solution Forum 2 ( UNIDO )
Global South-South Expo
A presentation from solution forum 2 organized by UNIDO.
Clean Technologies for Green Industry is the theme for this forum and is the United Nations Industrial Development Organization (UNIDO) important contribution to the Global South South Development Expo 2013. It will focus on showcasing clean technology solutions that have been successfully implemented in developing countries, emphasizing Southern-grown technologies, as well as South-South, North-South-South triangular cooperation and PPP modalities
Investor Overview Presentation
The document provides an overview of Rockwell Collins for investors for Q4 FY13. It summarizes Rockwell Collins' business segments which include avionics, communications products, and navigation products for commercial and military applications. It highlights the company's balanced business model and consistent financial performance through market cycles with 24% revenue CAGR and 12% EPS CAGR since 2002. The document also outlines the company's strengths in both government and commercial systems businesses and drivers for long-term growth.
Kb fkm-2011
Dokumen tersebut membahas tiga fase keluarga berencana yang mencakup usia dan metode kontrasepsi prioritas. Juga dibahas berbagai jenis metode kontrasepsi modern seperti pil kombinasi, injeksi, IUD, dan kontrasepsi mantap beserta prinsip kerja dan efek sampingnya.
GSSD 13 SOLUTION FORUM 1 (UNEP)
Global South- South Development Expo
A presentation from Solution Forum 1 by UNEP
Solution Forum 1 will present innovative Southern projects that are contributing substantial and tangible benefits to the environment as well as to economic development, decent job creation and poverty eradication at the global, regional and national levels.The forum will emphasize the crucial role that environmental considerations, when embedded in an adequate policy framework, can play in the transition to an inclusive green economy. In addition, it will showcase how South-South cooperation in the area of the environment can spur lasting change in the social and economic pillars of sustainable development.
Gray anatomia para_estudiantes_3_opt
Este documento presenta un libro de texto sobre anatomía humana dirigido a estudiantes. El libro se organiza en capítulos que cubren cada región anatómica de forma regional y clínica. Cada capítulo contiene secciones sobre conceptos generales, anatomía regional, anatomía de superficie y casos clínicos. El objetivo es proporcionar a los estudiantes la información anatómica fundamental de una forma integrada y orientada a la práctica clínica.
Recommended
DESeq Paper Journal club
DESeq models read counts with a negative binomial distribution to account for biological variability between samples, which a Poisson distribution underestimates. It estimates variance for each gene based on a local regression of variance against mean expression of other genes. This allows it to better control false positives compared to EdgeR or a Poisson model. DESeq also estimates sequencing depth differently than EdgeR to improve differential expression testing across the dynamic range of expression levels.
GSSD13 Solution Forum 2 ( UNIDO )
Global South-South Expo
A presentation from solution forum 2 organized by UNIDO.
Clean Technologies for Green Industry is the theme for this forum and is the United Nations Industrial Development Organization (UNIDO) important contribution to the Global South South Development Expo 2013. It will focus on showcasing clean technology solutions that have been successfully implemented in developing countries, emphasizing Southern-grown technologies, as well as South-South, North-South-South triangular cooperation and PPP modalities
Investor Overview Presentation
The document provides an overview of Rockwell Collins for investors for Q4 FY13. It summarizes Rockwell Collins' business segments which include avionics, communications products, and navigation products for commercial and military applications. It highlights the company's balanced business model and consistent financial performance through market cycles with 24% revenue CAGR and 12% EPS CAGR since 2002. The document also outlines the company's strengths in both government and commercial systems businesses and drivers for long-term growth.
Kb fkm-2011
Dokumen tersebut membahas tiga fase keluarga berencana yang mencakup usia dan metode kontrasepsi prioritas. Juga dibahas berbagai jenis metode kontrasepsi modern seperti pil kombinasi, injeksi, IUD, dan kontrasepsi mantap beserta prinsip kerja dan efek sampingnya.
GSSD 13 SOLUTION FORUM 1 (UNEP)
Global South- South Development Expo
A presentation from Solution Forum 1 by UNEP
Solution Forum 1 will present innovative Southern projects that are contributing substantial and tangible benefits to the environment as well as to economic development, decent job creation and poverty eradication at the global, regional and national levels.The forum will emphasize the crucial role that environmental considerations, when embedded in an adequate policy framework, can play in the transition to an inclusive green economy. In addition, it will showcase how South-South cooperation in the area of the environment can spur lasting change in the social and economic pillars of sustainable development.
Gray anatomia para_estudiantes_3_opt
Este documento presenta un libro de texto sobre anatomía humana dirigido a estudiantes. El libro se organiza en capítulos que cubren cada región anatómica de forma regional y clínica. Cada capítulo contiene secciones sobre conceptos generales, anatomía regional, anatomía de superficie y casos clínicos. El objetivo es proporcionar a los estudiantes la información anatómica fundamental de una forma integrada y orientada a la práctica clínica.
6 c flat plans
This document outlines the common elements found in newspaper and magazine layouts. It includes the masthead, cover lines, headlines, section headers, features, editorials, page numbers, captions, bylines, and sidebars that provide additional context or information to accompany articles. Graphics, photos, and pull quotes are integrated throughout the layout to highlight key points and engage readers.
GSSD13 Solution Forum 2 ( UNIDO)
Global South-South Expo
A presentation from solution forum 2 ( UNIDO )
Clean Technologies for Green Industry is the theme for this forum and is the United Nations Industrial Development Organization (UNIDO) important contribution to the Global South South Development Expo 2013. It will focus on showcasing clean technology solutions that have been successfully implemented in developing countries, emphasizing Southern-grown technologies, as well as South-South, North-South-South triangular cooperation and PPP modalities
Marbled zesty frog final
This document proposes an online marketplace called "Marbled" that would connect organic meat producers, businesses, and consumers in the UK. It would function as both an online farmer's market and auction house for organic British meat. The proposal outlines trends in organic local food consumption, potential revenue streams from commissions and subscriptions, forecasts projecting profitability, and marketing strategies to target various consumer demographics. Visualizations depict the planned mobile app and website user interfaces. The overall goal is to increase organic meat production in the UK through a digital community bringing all stakeholders together in one place.
HR Salon Bratislava
MUDr. Filip Brodan presented an analysis of 6,590 Czech employee psychological profiles with an average age of 36 years. The analysis found that employees primarily valued personal gain and stimulation over adapting to company values and rules. Unethical behavior aimed at personal profit rather than common company values was shown to lead to loss of motivation. Brodan encouraged trying an online assessment tool at www.balancemanagement.com to address these issues.
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of Excellence
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of ExcellenceGlobal South-South Development Expo
Global South-South Development Expo 2013
Solution Forum 6:
Development of green economies through regional action plans & PPP's
Description:
This Solution Exchange Forum on the “Development of Green Economies through Regional Action Plans and Public-Private Partnerships” will show how developing countries and countries with economies in transition could benefit from and make use of the Action Plans and approaches for public-private partnerships developed by UNECE to promote stronger and greener economies.
More about Solution Forum 6: http://j.mp/GSSDsf6Q1 fy16 quarterly earnings presentation
This document provides a summary of Rockwell Collins' financial results for the first quarter of fiscal year 2016. Key points include:
- Sales were down 5% to $1.169 billion compared to the same period last year, driven by lower OEM production rates in business aviation and lower military sales. Aftermarket sales increased 8%.
- Income from continuing operations decreased 21% to $133 million due to restructuring charges. Earnings per share also decreased 21% to $1.00.
- Guidance for full fiscal year 2016 expects total sales between $5.3-5.4 billion and earnings per share of $5.45-5.65.
Resume - David Lazarus 21.05.2015 - Demand Planner
David Lazarus is a 47-year-old South African male with experience implementing and supporting various ERP systems such as SAP, Lawson, and Syspro. He currently works as a demand planner for On the Dot Media. He has a diploma in logistics and degrees in commerce and economics. Lazarus seeks to further his SAP certification and sales leadership skills.
Reporte sobre los animales invertebrados
Este documento presenta información sobre animales invertebrados. En la primera parte, define a los invertebrados como animales sin columna vertebral ni esqueleto interno, y clasifica los principales grupos de invertebrados. Luego, describe las características y ejemplos de artrópodos, moluscos y equinodermos. En las partes siguientes, explica conceptos como reproducción, tipos de células, características generales y ejemplos de invertebrados.
A2 Media Evaluation Question 1
The document discusses the conventions of social realism films that the media product adheres to and challenges. It outlines that social realism films typically explore urban issues, use working class characters in impoverished settings, and feature rebels who don't conform to rules. The media product manages to adhere to these conventions to clearly be recognized as a social realism genre film. However, it also challenges conventions by including a strong moral message about family being important, which contrasts with how family is sometimes portrayed in other social realism films.
Práctica 5 integración metabólica
Este documento presenta los resultados de un estudio que midió los niveles de glucosa, triglicéridos, ácido úrico y colesterol en la sangre de 5 estudiantes entre 18 y 20 años. Los resultados mostraron que una estudiante tenía niveles normales en todas las mediciones, mientras que los demás estudiantes tenían niveles anormales de uno o más biomarcadores. El documento analiza cómo factores como la dieta, el peso, las enfermedades y el estilo de vida pueden afectar los niveles sanguíneos.
Col credit suisse industrials conference final
Rockwell Collins presented at a credit suisse investor conference to discuss their acquisition of ARINC. The summary is:
1) Rockwell Collins provides avionics, communications and electronics products for both commercial and military aviation. They see opportunities to accelerate growth through the acquisition of ARINC.
2) ARINC provides aviation information management services including connectivity, content and applications. The combination with Rockwell Collins will allow them to offer more integrated end-to-end solutions.
3) Synergies from the acquisition include revenue opportunities from expanded services and cost savings from consolidating functions. ARINC is expected to increase Rockwell Collins' sales growth and cash flow.
Nano plastic
The document proposes manufacturing and selling nano-plastic pieces to strengthen cement and make concrete more waterproof. Adding plastic would make cement cheaper and more durable than standard concrete. Selling raw nano-plastic separately from cement would allow customers to mix their own batches according to provided instructions and prevent material loss when opening bags.
Dràcula
Abraham Stoker fue un escritor irlandés nacido en 1847 que es mejor conocido por escribir la novela Drácula en 1897. Drácula, publicada epistolarmente, presenta el famoso conde vampiro y explora temas como el rol de la mujer victoriana, la sexualidad y el folklore, además de convertirse en una de las historias de terror más influyentes de todos los tiempos. Stoker se basó en conversaciones con el erudito húngaro Arminius Vámbéry sobre Vlad Drăculea para crear al personaje.
Programming in Computational Biology
This document discusses the role of programming in computational biology. It begins by describing different types of programming languages like imperative, object-oriented, and functional languages. It then discusses how programming can reduce time, money, effort and errors in computational biology applications. Some key applications of programming in computational biology mentioned are data mining, genome annotation, microarray analysis, phylogenetics, and next generation sequencing studies. The document also discusses popular bioinformatics programming languages like Perl and describes concepts in programming like objects, modules, and the common gateway interface.
Comparison Of Commercially Available Str Typing Kits (Nx Power Lite)
The document compares the accuracy and efficacy of commercially available STR typing kits from Applied Biosystems and Promega Corporation using various samples. Studies found that while the kits performed reasonably well on low copy number samples, allelic dropout rates were around 7-14% on average. Optimal DNA sample size for profiling was determined to be around 1-2ng. Motherless paternity testing using one kit produced non-definitive results in over half of cases compared to standard trio testing. Degraded DNA samples showed some loci produced more valid results depending on the kit.
Towards Ultra-Large-Scale System: Design of Scalable Software and Next-Gen H...
Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing. Consequently, scientists are in dire need of robust high-performance computing (HPC) solutions that can scale with terabytes of data.
In this talk, I will address the challenges of two major aspects of scientific big data processing: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures that these applications and software tools need for good performance. In this talk, I will mainly address the challenges involved in large-scale genome analysis applications such as, genomic error correction and genome assembly which made their way to the forefront of big data challenges recently as the sequencing machines outperformed Moore's law by several magnitudes.
In the first part, I will address the challenges involved in developing scalable algorithms to process huge amounts of genomic big data using the power of recent analytic tools such as, Hadoop, Giraph, distributed NoSQL, etc. The algorithms are carefully tailored to scale over terabytes of data over hundreds of computing nodes. At a border level, these algorithms take advantage of locality-based computing for their scalability. In this aspect, I will briefly talk about my general-purpose, analytic framework for easy and rapid designing of embarrassingly parallel algorithms for massive-scale scientific data.
In the second part, I will address the challenges in designing the hardware environment that these data- and compute-intensive applications require for good performance. I will pinpoint the limitations in a traditional HPC cluster (supercomputer) to process this huge amount of big genomic data with respect to these applications and propose a solution to those limitations by balancing the storage (both I/O and memory) bandwidth, with the computational speed of high-performance CPUs. I will briefly discuss my theoretical model that can help the HPC system designers who are striving for system balance.
Many of these observations and developments are used by different hardware vendors such as, Samsung and IBM to develop or improve the configuration of their next-gen HPC clusters (e.g., Samsung’s hyper-scale computing cluster, IBM’s Power8-based supercomputer) with high-speed storage and processing power
MidtermReview.pdfStatistics 411511Important Concepts an.docx
MidtermReview.pdf
Statistics 411/511
Important Concepts and Tasks for the Midterm
(Not Necessarily in any Order)
Scope of Material for Midterm
The midterm will cover the material in Chapter 1 through Section 5.5, excluding Section 5.4
and the parts of Chapter 4 noted in item 4(a) below.
1. Two-sample t-test.
(a) Know assumptions, and assess their validity from graphical displays such as boxplots
and histograms.
(b) Given R output, write a brief (one or two sentences) statistical summary reporting results.
(c) Given summary statistics, write the t-statistic (this may entail calculating the pooled
standard deviation).
(d) Given summary statistics and a confidence level, write a confidence interval.
(e) Know how to find the degrees of freedom of the pooled standard deviation.
(f) Decide if a one-tailed or two-tailed test is most appropriate.
(g) Suggest a procedure to use when the equal-variance assumption is not met.
(h) Given R t.test() output, be able to tell if test was one- or two-sided and if equal
variance assumption was made or not.
2. Paired t-test
(a) Know when to use a paired t-test as opposed to a two-sample t-test.
(b) Know assumptions, and assess their validity from graphical displays such as boxplots
and histograms.
(c) Given R output, write a brief statistical summary reporting results.
(d) Given summary statistics, write the t-statistic.
(e) Given summary statistics and a confidence level, write a confidence interval.
(f) Decide if a one-tailed or two-tailed test is most appropriate.
3. Transformations
(a) Know when log or logit are appropriate transformations to consider.
(b) Back-transform and interpret results on the original scale after a log transformation.
4. Non-parametric Alternatives to t-tests
(a) We skipped the signed-rank test, so you should be familiar with the Wilcoxon rank-sum
test, Welch’s t-test, permutation/randomization tests, and the sign test. You can ignore
Levene’s test for the exam.
(b) Given a study, decide which procedures is/are appropriate.
1
(c) Given R output, write a brief statistical summary reporting results.
(d) Know the mean and standard deviation of the normal approximation to the sampling
distribution of the Wilcoxon rank-sum test statistic T or the sign test statistic K.
(e) Understand the principle behind a permutation/randomization test. (Technically, a per-
mutation test considers ALL random shufflings of the data, whereas a randomization test
just considers a large number of them. The test on the space shuttle O-ring in Section
4.3.1 is a permutation test. The test on the creativity study data in Section 1.3.2 is a
randomization test.)
5. One-way Analysis of Variance (ANOVA)
(a) Know assumptions and assess their validity from side-by-side boxplots or a residual plot.
(b) Given R anova() output, calculate the pooled standard deviation.
(c) Given R anova() output, find the degrees of freedom associated with a pooled standard
deviation.
(d) Given R anova ...
Quantifiler® Trio kit and forensic samples management: a matter of degradation
Quantifiler® Trio kit and forensic samples management: a matter of degradationThermo Fisher Scientific
"Quantifiler® Trio kit and forensic samples management: a matter of degradation
Stefano Vernarecci
Forensic Genetics Laboratory
Scientific Police Service
Department of Ministry of Interior
Rome, Italy
Human Identification Solutions Conference – Madrid, Spain
March 4, 2015
Quantifiler® Trio DNA Quantification Kit
* Evaluate the reliability of the Quantifiler® Trio kit in providing information
on the level of degradation in a sample.
* Study the opportunity to use this information in predicting the quality of
the profile obtained after genotyping.
* Define operative implications, taking into account the DI, to apply to our
routine analysis in order to choose the best PCR strategy when dealing with
degraded samples
Please see also:
http://www.fsigenetics.com/article/S1872-4973(14)00280-4/abstract"Interpreting Logistic Regression.pptx
This document discusses logistic regression for categorical response variables. It provides examples of binary and ordinal categorical response variables like whether someone smokes (yes/no) or the success of a medical treatment (survives/dies). It then demonstrates how to perform binary logistic regression in R to predict a binary outcome like gender from height. Key aspects covered include interpreting the logistic regression coefficients, plotting the logistic curve, and calculating odds ratios to compare two groups.
Teaching Population Genetics with R
Presented at Evolution 2013, June 24; describes an approach to teaching populations genetics at the upper undergraduate/beginning graduate level, using simulations based in R and incorporating available large genomic data sets.
More Related Content
Viewers also liked
6 c flat plans
This document outlines the common elements found in newspaper and magazine layouts. It includes the masthead, cover lines, headlines, section headers, features, editorials, page numbers, captions, bylines, and sidebars that provide additional context or information to accompany articles. Graphics, photos, and pull quotes are integrated throughout the layout to highlight key points and engage readers.
GSSD13 Solution Forum 2 ( UNIDO)
Global South-South Expo
A presentation from solution forum 2 ( UNIDO )
Clean Technologies for Green Industry is the theme for this forum and is the United Nations Industrial Development Organization (UNIDO) important contribution to the Global South South Development Expo 2013. It will focus on showcasing clean technology solutions that have been successfully implemented in developing countries, emphasizing Southern-grown technologies, as well as South-South, North-South-South triangular cooperation and PPP modalities
Marbled zesty frog final
This document proposes an online marketplace called "Marbled" that would connect organic meat producers, businesses, and consumers in the UK. It would function as both an online farmer's market and auction house for organic British meat. The proposal outlines trends in organic local food consumption, potential revenue streams from commissions and subscriptions, forecasts projecting profitability, and marketing strategies to target various consumer demographics. Visualizations depict the planned mobile app and website user interfaces. The overall goal is to increase organic meat production in the UK through a digital community bringing all stakeholders together in one place.
HR Salon Bratislava
MUDr. Filip Brodan presented an analysis of 6,590 Czech employee psychological profiles with an average age of 36 years. The analysis found that employees primarily valued personal gain and stimulation over adapting to company values and rules. Unethical behavior aimed at personal profit rather than common company values was shown to lead to loss of motivation. Brodan encouraged trying an online assessment tool at www.balancemanagement.com to address these issues.
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of Excellence
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of ExcellenceGlobal South-South Development Expo
Global South-South Development Expo 2013
Solution Forum 6:
Development of green economies through regional action plans & PPP's
Description:
This Solution Exchange Forum on the “Development of Green Economies through Regional Action Plans and Public-Private Partnerships” will show how developing countries and countries with economies in transition could benefit from and make use of the Action Plans and approaches for public-private partnerships developed by UNECE to promote stronger and greener economies.
More about Solution Forum 6: http://j.mp/GSSDsf6Q1 fy16 quarterly earnings presentation
This document provides a summary of Rockwell Collins' financial results for the first quarter of fiscal year 2016. Key points include:
- Sales were down 5% to $1.169 billion compared to the same period last year, driven by lower OEM production rates in business aviation and lower military sales. Aftermarket sales increased 8%.
- Income from continuing operations decreased 21% to $133 million due to restructuring charges. Earnings per share also decreased 21% to $1.00.
- Guidance for full fiscal year 2016 expects total sales between $5.3-5.4 billion and earnings per share of $5.45-5.65.
Resume - David Lazarus 21.05.2015 - Demand Planner
David Lazarus is a 47-year-old South African male with experience implementing and supporting various ERP systems such as SAP, Lawson, and Syspro. He currently works as a demand planner for On the Dot Media. He has a diploma in logistics and degrees in commerce and economics. Lazarus seeks to further his SAP certification and sales leadership skills.
Reporte sobre los animales invertebrados
Este documento presenta información sobre animales invertebrados. En la primera parte, define a los invertebrados como animales sin columna vertebral ni esqueleto interno, y clasifica los principales grupos de invertebrados. Luego, describe las características y ejemplos de artrópodos, moluscos y equinodermos. En las partes siguientes, explica conceptos como reproducción, tipos de células, características generales y ejemplos de invertebrados.
A2 Media Evaluation Question 1
The document discusses the conventions of social realism films that the media product adheres to and challenges. It outlines that social realism films typically explore urban issues, use working class characters in impoverished settings, and feature rebels who don't conform to rules. The media product manages to adhere to these conventions to clearly be recognized as a social realism genre film. However, it also challenges conventions by including a strong moral message about family being important, which contrasts with how family is sometimes portrayed in other social realism films.
Práctica 5 integración metabólica
Este documento presenta los resultados de un estudio que midió los niveles de glucosa, triglicéridos, ácido úrico y colesterol en la sangre de 5 estudiantes entre 18 y 20 años. Los resultados mostraron que una estudiante tenía niveles normales en todas las mediciones, mientras que los demás estudiantes tenían niveles anormales de uno o más biomarcadores. El documento analiza cómo factores como la dieta, el peso, las enfermedades y el estilo de vida pueden afectar los niveles sanguíneos.
Col credit suisse industrials conference final
Rockwell Collins presented at a credit suisse investor conference to discuss their acquisition of ARINC. The summary is:
1) Rockwell Collins provides avionics, communications and electronics products for both commercial and military aviation. They see opportunities to accelerate growth through the acquisition of ARINC.
2) ARINC provides aviation information management services including connectivity, content and applications. The combination with Rockwell Collins will allow them to offer more integrated end-to-end solutions.
3) Synergies from the acquisition include revenue opportunities from expanded services and cost savings from consolidating functions. ARINC is expected to increase Rockwell Collins' sales growth and cash flow.
Nano plastic
The document proposes manufacturing and selling nano-plastic pieces to strengthen cement and make concrete more waterproof. Adding plastic would make cement cheaper and more durable than standard concrete. Selling raw nano-plastic separately from cement would allow customers to mix their own batches according to provided instructions and prevent material loss when opening bags.
Dràcula
Abraham Stoker fue un escritor irlandés nacido en 1847 que es mejor conocido por escribir la novela Drácula en 1897. Drácula, publicada epistolarmente, presenta el famoso conde vampiro y explora temas como el rol de la mujer victoriana, la sexualidad y el folklore, además de convertirse en una de las historias de terror más influyentes de todos los tiempos. Stoker se basó en conversaciones con el erudito húngaro Arminius Vámbéry sobre Vlad Drăculea para crear al personaje.
Viewers also liked (15)
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of Excellence
GSSD 13 Solution Forum 6 (UNECE) - UNECE International PPP Centre of Excellence
Resume - David Lazarus 21.05.2015 - Demand Planner
Resume - David Lazarus 21.05.2015 - Demand Planner
Similar to Brendel Group Presentation: 17 Oct 2013
Programming in Computational Biology
This document discusses the role of programming in computational biology. It begins by describing different types of programming languages like imperative, object-oriented, and functional languages. It then discusses how programming can reduce time, money, effort and errors in computational biology applications. Some key applications of programming in computational biology mentioned are data mining, genome annotation, microarray analysis, phylogenetics, and next generation sequencing studies. The document also discusses popular bioinformatics programming languages like Perl and describes concepts in programming like objects, modules, and the common gateway interface.
Comparison Of Commercially Available Str Typing Kits (Nx Power Lite)
The document compares the accuracy and efficacy of commercially available STR typing kits from Applied Biosystems and Promega Corporation using various samples. Studies found that while the kits performed reasonably well on low copy number samples, allelic dropout rates were around 7-14% on average. Optimal DNA sample size for profiling was determined to be around 1-2ng. Motherless paternity testing using one kit produced non-definitive results in over half of cases compared to standard trio testing. Degraded DNA samples showed some loci produced more valid results depending on the kit.
Towards Ultra-Large-Scale System: Design of Scalable Software and Next-Gen H...
Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing. Consequently, scientists are in dire need of robust high-performance computing (HPC) solutions that can scale with terabytes of data.
In this talk, I will address the challenges of two major aspects of scientific big data processing: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures that these applications and software tools need for good performance. In this talk, I will mainly address the challenges involved in large-scale genome analysis applications such as, genomic error correction and genome assembly which made their way to the forefront of big data challenges recently as the sequencing machines outperformed Moore's law by several magnitudes.
In the first part, I will address the challenges involved in developing scalable algorithms to process huge amounts of genomic big data using the power of recent analytic tools such as, Hadoop, Giraph, distributed NoSQL, etc. The algorithms are carefully tailored to scale over terabytes of data over hundreds of computing nodes. At a border level, these algorithms take advantage of locality-based computing for their scalability. In this aspect, I will briefly talk about my general-purpose, analytic framework for easy and rapid designing of embarrassingly parallel algorithms for massive-scale scientific data.
In the second part, I will address the challenges in designing the hardware environment that these data- and compute-intensive applications require for good performance. I will pinpoint the limitations in a traditional HPC cluster (supercomputer) to process this huge amount of big genomic data with respect to these applications and propose a solution to those limitations by balancing the storage (both I/O and memory) bandwidth, with the computational speed of high-performance CPUs. I will briefly discuss my theoretical model that can help the HPC system designers who are striving for system balance.
Many of these observations and developments are used by different hardware vendors such as, Samsung and IBM to develop or improve the configuration of their next-gen HPC clusters (e.g., Samsung’s hyper-scale computing cluster, IBM’s Power8-based supercomputer) with high-speed storage and processing power
MidtermReview.pdfStatistics 411511Important Concepts an.docx
MidtermReview.pdf
Statistics 411/511
Important Concepts and Tasks for the Midterm
(Not Necessarily in any Order)
Scope of Material for Midterm
The midterm will cover the material in Chapter 1 through Section 5.5, excluding Section 5.4
and the parts of Chapter 4 noted in item 4(a) below.
1. Two-sample t-test.
(a) Know assumptions, and assess their validity from graphical displays such as boxplots
and histograms.
(b) Given R output, write a brief (one or two sentences) statistical summary reporting results.
(c) Given summary statistics, write the t-statistic (this may entail calculating the pooled
standard deviation).
(d) Given summary statistics and a confidence level, write a confidence interval.
(e) Know how to find the degrees of freedom of the pooled standard deviation.
(f) Decide if a one-tailed or two-tailed test is most appropriate.
(g) Suggest a procedure to use when the equal-variance assumption is not met.
(h) Given R t.test() output, be able to tell if test was one- or two-sided and if equal
variance assumption was made or not.
2. Paired t-test
(a) Know when to use a paired t-test as opposed to a two-sample t-test.
(b) Know assumptions, and assess their validity from graphical displays such as boxplots
and histograms.
(c) Given R output, write a brief statistical summary reporting results.
(d) Given summary statistics, write the t-statistic.
(e) Given summary statistics and a confidence level, write a confidence interval.
(f) Decide if a one-tailed or two-tailed test is most appropriate.
3. Transformations
(a) Know when log or logit are appropriate transformations to consider.
(b) Back-transform and interpret results on the original scale after a log transformation.
4. Non-parametric Alternatives to t-tests
(a) We skipped the signed-rank test, so you should be familiar with the Wilcoxon rank-sum
test, Welch’s t-test, permutation/randomization tests, and the sign test. You can ignore
Levene’s test for the exam.
(b) Given a study, decide which procedures is/are appropriate.
1
(c) Given R output, write a brief statistical summary reporting results.
(d) Know the mean and standard deviation of the normal approximation to the sampling
distribution of the Wilcoxon rank-sum test statistic T or the sign test statistic K.
(e) Understand the principle behind a permutation/randomization test. (Technically, a per-
mutation test considers ALL random shufflings of the data, whereas a randomization test
just considers a large number of them. The test on the space shuttle O-ring in Section
4.3.1 is a permutation test. The test on the creativity study data in Section 1.3.2 is a
randomization test.)
5. One-way Analysis of Variance (ANOVA)
(a) Know assumptions and assess their validity from side-by-side boxplots or a residual plot.
(b) Given R anova() output, calculate the pooled standard deviation.
(c) Given R anova() output, find the degrees of freedom associated with a pooled standard
deviation.
(d) Given R anova ...
Quantifiler® Trio kit and forensic samples management: a matter of degradation
Quantifiler® Trio kit and forensic samples management: a matter of degradationThermo Fisher Scientific
"Quantifiler® Trio kit and forensic samples management: a matter of degradation
Stefano Vernarecci
Forensic Genetics Laboratory
Scientific Police Service
Department of Ministry of Interior
Rome, Italy
Human Identification Solutions Conference – Madrid, Spain
March 4, 2015
Quantifiler® Trio DNA Quantification Kit
* Evaluate the reliability of the Quantifiler® Trio kit in providing information
on the level of degradation in a sample.
* Study the opportunity to use this information in predicting the quality of
the profile obtained after genotyping.
* Define operative implications, taking into account the DI, to apply to our
routine analysis in order to choose the best PCR strategy when dealing with
degraded samples
Please see also:
http://www.fsigenetics.com/article/S1872-4973(14)00280-4/abstract"Interpreting Logistic Regression.pptx
This document discusses logistic regression for categorical response variables. It provides examples of binary and ordinal categorical response variables like whether someone smokes (yes/no) or the success of a medical treatment (survives/dies). It then demonstrates how to perform binary logistic regression in R to predict a binary outcome like gender from height. Key aspects covered include interpreting the logistic regression coefficients, plotting the logistic curve, and calculating odds ratios to compare two groups.
Teaching Population Genetics with R
Presented at Evolution 2013, June 24; describes an approach to teaching populations genetics at the upper undergraduate/beginning graduate level, using simulations based in R and incorporating available large genomic data sets.
6 sigma
This document provides information on calculating process capability indices Cp, Cpk, Pp, and Ppk. It defines the standard deviation formulas for short-term and long-term data. For short-term data, it calculates Cp as 1.938 and Cpk as 1.919 using sample data. For long-term data, it calculates Pp as 1.75 and Ppk as 1.81. It also includes histograms and tables to help explain the concepts and calculations.
LargeRDFBench: A billion triples benchmark for SPARQL endpoint federation
LargeRDFBench: A billion triples benchmark for SPARQL endpoint federationHolistic Benchmarking of Big Linked Data
"LargeRDFBench: A billion triples benchmark for SPARQL endpoint federation" as presented in the 17th International Semantic Web Conference ISWC ( ournal track), 8th - 12th of October 2018, held in Monterey, California, USA
This work was supported by grants from the EU H2020 Framework Programme provided for the project HOBBIT (GA no. 688227).Presentation R basic teaching module
This document provides an introduction to the statistical programming language R. It outlines what R is, how to access and use its interface, and how to work with basic data types like vectors, matrices, and factors. It also demonstrates how to import and export data, perform basic plotting and graphics, and gives examples working with biological data from Affymetrix chips. The presenter encourages attendees to ask questions and notes they are not a perfect teacher.
PASCAL PASCAL CHALLENGE ON INFORMATION EXTRACTION
The document summarizes the Pascal Challenge on Information Extraction and Machine Learning. The challenge involved several tasks related to extracting information from workshop and conference announcements using machine learning techniques. Participants used various algorithms like SVM, CRF, HMM and rule induction to complete the tasks. The top performing systems used different algorithms and the same algorithms did not always produce consistent results. Learning curve and active learning tasks provided insights into how performance varies with training data and selection methods.
www1.cs.columbia.edu
Machine learning algorithms can learn through supervised, unsupervised, or reinforcement learning. Supervised learning involves providing labeled examples to learn a function that maps inputs to outputs. Unsupervised learning identifies hidden patterns in unlabeled data. Reinforcement learning involves an agent learning through trial-and-error interactions with a dynamic environment. Machine learning has applications in areas like computer vision, natural language processing, medical diagnosis, and more.
3 Ways the New Thermo Scientific LC MS Triple Quads Improve Residue Analysis
3 Ways the New Thermo Scientific LC MS Triple Quads Improve Residue AnalysisThermo Fisher Scientific
Learn how the new Thermo Scientific LC-MS triple quadrupole mass spectrometers incorporate unique design features that improve analysis of food matrices for veterinary drug and pesticide residues. Clinicaldataanalysis in r
This document describes using R to analyze clinical trial data to compare the effects of a new drug (Treatment A) versus placebo (Treatment B) on diastolic blood pressure (DBP) over time. Statistical tests conducted include t-tests, ANOVA, bootstrapping, and multiple comparisons. The analysis found Treatment A significantly lowered DBP more than the placebo over the 4 month trial period.
Similar to Brendel Group Presentation: 17 Oct 2013 (14)
Comparison Of Commercially Available Str Typing Kits (Nx Power Lite)
Comparison Of Commercially Available Str Typing Kits (Nx Power Lite)
Towards Ultra-Large-Scale System: Design of Scalable Software and Next-Gen H...
Towards Ultra-Large-Scale System: Design of Scalable Software and Next-Gen H...
MidtermReview.pdfStatistics 411511Important Concepts an.docx
MidtermReview.pdfStatistics 411511Important Concepts an.docx
Quantifiler® Trio kit and forensic samples management: a matter of degradation
Quantifiler® Trio kit and forensic samples management: a matter of degradation
LargeRDFBench: A billion triples benchmark for SPARQL endpoint federation
LargeRDFBench: A billion triples benchmark for SPARQL endpoint federation
3 Ways the New Thermo Scientific LC MS Triple Quads Improve Residue Analysis
3 Ways the New Thermo Scientific LC MS Triple Quads Improve Residue Analysis
More from danielstandage
Brendel Group Presentation: 6 Mar 2013
The document compares different assembly algorithms for constructing transcripts from RNA-seq data: Butterfly, PASA, and CuffLinks. It analyzes eight assemblies that vary the algorithm and use of digital normalization. Butterfly produced the most transcripts while PASA and CuffLinks were more conservative. PASA and CuffLinks assemblies were more robust to digital normalization. The document proposes additional statistical analyses and using an expectation-maximization algorithm to discern isoforms.
Brendel Group Presentation: 4 Mar 2013
The document discusses three algorithms for reconstructing transcripts from RNA-Seq data that are available in the Trinity RNA-Seq package: Butterfly, PASA, and Cufflinks. Butterfly aims to enumerate all plausible transcripts supported by reads, PASA finds the largest assembly containing each alignment, and Cufflinks identifies the minimal set of transcripts needed to explain the read mappings. The presentation will next compare results from running Trinity with these three algorithms on two different RNA-Seq datasets.
Brendel Group Presentation: 21 Nov 2013
The document summarizes Daniel Standage's analysis of differential gene expression in the paper wasp Polistes dominula. He performed locus-level differential expression analysis after isoform-level analysis proved unreliable. The genome contains 18,675 intervals (iLoci) partitioned by gene content. Initial analysis found 295 differentially expressed iLoci but sample grouping was problematic. After filtering iLoci by read counts and re-running the analysis without a problematic sample, 314 differentially expressed iLoci were identified, mostly over-expressed in workers. Cytochrome P450 and NADH dehydrogenase genes were frequently differentially expressed.
Brendel Group Presentation: 19 Nov 2013
The document discusses cytochrome P450 (CYP) genes that were found in the genome of the paper wasp Polistes dominula. CYP genes encode oxidation enzymes and play important roles in insects, including metabolizing exogenous compounds and regulating endogenous compounds like juvenile hormone and ecdysone. The analysis of P. dominula found many differentially expressed CYP genes. CYP genes have been associated with caste determination in other social insects through their links to juvenile hormone.
Brendel Group Presentation: 5 Nov 2013
Slides from my debriefing of the Cold Spring Harbor Lab Genome Informatics meeting I attended 30 Oct-2 Nov 2013.
Brendel Group Presentation: 15 Oct 2013
This document discusses RSEM, a tool for accurate transcript quantification from RNA-seq data. RSEM uses expectation maximization to estimate transcript expression levels without requiring a reference genome. It handles multireads better than other tools by either discarding, rescuing, or estimating maximum likelihood expression levels. Evaluation on simulated data showed RSEM had higher accuracy than other tools like Cufflinks and rQuant.
More from danielstandage (6)
Recently uploaded
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AI
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AIVladimir Iglovikov, Ph.D.
Presented by Vladimir Iglovikov:
- https://www.linkedin.com/in/iglovikov/
- https://x.com/viglovikov
- https://www.instagram.com/ternaus/
This presentation delves into the journey of Albumentations.ai, a highly successful open-source library for data augmentation.
Created out of a necessity for superior performance in Kaggle competitions, Albumentations has grown to become a widely used tool among data scientists and machine learning practitioners.
This case study covers various aspects, including:
People: The contributors and community that have supported Albumentations.
Metrics: The success indicators such as downloads, daily active users, GitHub stars, and financial contributions.
Challenges: The hurdles in monetizing open-source projects and measuring user engagement.
Development Practices: Best practices for creating, maintaining, and scaling open-source libraries, including code hygiene, CI/CD, and fast iteration.
Community Building: Strategies for making adoption easy, iterating quickly, and fostering a vibrant, engaged community.
Marketing: Both online and offline marketing tactics, focusing on real, impactful interactions and collaborations.
Mental Health: Maintaining balance and not feeling pressured by user demands.
Key insights include the importance of automation, making the adoption process seamless, and leveraging offline interactions for marketing. The presentation also emphasizes the need for continuous small improvements and building a friendly, inclusive community that contributes to the project's growth.
Vladimir Iglovikov brings his extensive experience as a Kaggle Grandmaster, ex-Staff ML Engineer at Lyft, sharing valuable lessons and practical advice for anyone looking to enhance the adoption of their open-source projects.
Explore more about Albumentations and join the community at:
GitHub: https://github.com/albumentations-team/albumentations
Website: https://albumentations.ai/
LinkedIn: https://www.linkedin.com/company/100504475
Twitter: https://x.com/albumentationsLet's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slack
Discover the seamless integration of RPA (Robotic Process Automation), COMPOSER, and APM with AWS IDP enhanced with Slack notifications. Explore how these technologies converge to streamline workflows, optimize performance, and ensure secure access, all while leveraging the power of AWS IDP and real-time communication via Slack notifications.
“I’m still / I’m still / Chaining from the Block”
“An Outlook of the Ongoing and Future Relationship between Blockchain Technologies and Process-aware Information Systems.” Invited talk at the joint workshop on Blockchain for Information Systems (BC4IS) and Blockchain for Trusted Data Sharing (B4TDS), co-located with with the 36th International Conference on Advanced Information Systems Engineering (CAiSE), 3 June 2024, Limassol, Cyprus.
20240605 QFM017 Machine Intelligence Reading List May 2024
Everything I found interesting about machines behaving intelligently during May 2024
TrustArc Webinar - 2024 Global Privacy Survey
How does your privacy program stack up against your peers? What challenges are privacy teams tackling and prioritizing in 2024?
In the fifth annual Global Privacy Benchmarks Survey, we asked over 1,800 global privacy professionals and business executives to share their perspectives on the current state of privacy inside and outside of their organizations. This year’s report focused on emerging areas of importance for privacy and compliance professionals, including considerations and implications of Artificial Intelligence (AI) technologies, building brand trust, and different approaches for achieving higher privacy competence scores.
See how organizational priorities and strategic approaches to data security and privacy are evolving around the globe.
This webinar will review:
- The top 10 privacy insights from the fifth annual Global Privacy Benchmarks Survey
- The top challenges for privacy leaders, practitioners, and organizations in 2024
- Key themes to consider in developing and maintaining your privacy program
Microsoft - Power Platform_G.Aspiotis.pdf
Revolutionizing Application Development
with AI-powered low-code, presentation by George Aspiotis, Sr. Partner Development Manager, Microsoft
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024
Neha Bajwa, Vice President of Product Marketing, Neo4j
Join us as we explore breakthrough innovations enabled by interconnected data and AI. Discover firsthand how organizations use relationships in data to uncover contextual insights and solve our most pressing challenges – from optimizing supply chains, detecting fraud, and improving customer experiences to accelerating drug discoveries.
Large Language Model (LLM) and it’s Geospatial Applications
Large Language Model (LLM) and it’s Geospatial Applications.
20240609 QFM020 Irresponsible AI Reading List May 2024
Everything I found interesting about the irresponsible use of machine intelligence in May 2024
A tale of scale & speed: How the US Navy is enabling software delivery from l...
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
Pushing the limits of ePRTC: 100ns holdover for 100 days
At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
Essentials of Automations: The Art of Triggers and Actions in FME
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
Introducing Milvus Lite: Easy-to-Install, Easy-to-Use vector database for you...
Join us to introduce Milvus Lite, a vector database that can run on notebooks and laptops, share the same API with Milvus, and integrate with every popular GenAI framework. This webinar is perfect for developers seeking easy-to-use, well-integrated vector databases for their GenAI apps.
GraphSummit Singapore | Neo4j Product Vision & Roadmap - Q2 2024
Maruthi Prithivirajan, Head of ASEAN & IN Solution Architecture, Neo4j
Get an inside look at the latest Neo4j innovations that enable relationship-driven intelligence at scale. Learn more about the newest cloud integrations and product enhancements that make Neo4j an essential choice for developers building apps with interconnected data and generative AI.
Uni Systems Copilot event_05062024_C.Vlachos.pdf
Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
Removing Uninteresting Bytes in Software Fuzzing
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
UiPath Test Automation using UiPath Test Suite series, part 6
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Mind map of terminologies used in context of Generative AI
Mind map of common terms used in context of Generative AI.
Recently uploaded (20)
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AI
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AI
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slack
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slack
20240605 QFM017 Machine Intelligence Reading List May 2024
20240605 QFM017 Machine Intelligence Reading List May 2024
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024
Large Language Model (LLM) and it’s Geospatial Applications
Large Language Model (LLM) and it’s Geospatial Applications
20240609 QFM020 Irresponsible AI Reading List May 2024
20240609 QFM020 Irresponsible AI Reading List May 2024
A tale of scale & speed: How the US Navy is enabling software delivery from l...
A tale of scale & speed: How the US Navy is enabling software delivery from l...
Pushing the limits of ePRTC: 100ns holdover for 100 days
Pushing the limits of ePRTC: 100ns holdover for 100 days
Essentials of Automations: The Art of Triggers and Actions in FME
Essentials of Automations: The Art of Triggers and Actions in FME
Introducing Milvus Lite: Easy-to-Install, Easy-to-Use vector database for you...
Introducing Milvus Lite: Easy-to-Install, Easy-to-Use vector database for you...
GraphSummit Singapore | Neo4j Product Vision & Roadmap - Q2 2024
GraphSummit Singapore | Neo4j Product Vision & Roadmap - Q2 2024
UiPath Test Automation using UiPath Test Suite series, part 6
UiPath Test Automation using UiPath Test Suite series, part 6
Mind map of terminologies used in context of Generative AI
Mind map of terminologies used in context of Generative AI
Brendel Group Presentation: 17 Oct 2013
- 1. Differential expression in the paper wasp Polistes dominula Daniel S. Standage, Brendel Group Meeting, 17 Oct 2013
- 2. Experimental design 6 queen samples 6 worker samples Queen x and worker x from same colony (x ∈ [1 .. 6]) Hypothesis: identify handful of critical caste-related genes/transcripts
- 3. Initial (naïve) analysis with RSEM/EBSeq 209,675 transcripts (assembled by Trinity) RSEM and EBSeq completed without warnings 80-85% reads mapped Many DE transcripts reported 5,769 (FDR=.05) 4,763 (FDR=.01) 3,878 (FDR=.001)
- 4. Permutation testing Randomly shuffle caste labels (queen or worker) Re-run differential expression analysis Repeat test Compare number of transcripts reported as DE for each permutation https://github.com/standage/dept
- 5. Permutation testing Real data 4,763 (FDR=.01) Permutation 1 5,112 Permutation 2 4,174 Permutation 3 4,474 Permutation 4 4,307 Permutation 5 4,718 Permutation 6 4,312 Permutation 7 4,171 Permutation 8 4,714 Permutation 9 3,828 Permutation 10 5,192
- 6. Some observations Some expression levels very low Some transcripts had very few reads mapped Some transcripts had many read mapped Difficulty normalizing over large dynamic range?
- 7. Filter transcripts Reads mapped queen/worker reads mapped > 2,500 overall reads < 1,000,000 Samples 4+ queen/worker samples with > 0 reads mapped Distribution of reads mapped mean(queen/worker reads mapped) * 0.9 > stdev(queen/worker reads mapped)
- 8. DE analysis on filtered transcripts 40,498 transcripts RSEM/EBSeq completed without warnings 20-35% reads mapped Still many DE transcripts reported 1,680 (FDR=.05) 1,328 (FDR=.01) 1,037 (FDR=.001)
- 9. PdomTSAr1.1-034114 (FC=126) Sample Expression Reads mapped Reads (adjusted) Q1 0.00 5232 5669.09 Q2 0.00 10046 5148.89 Q3 51.18 9188 6644.97 Q4 136.68 7920 6901.36 Q5 698.51 27862 6712.76 Q6 0.00 2582 5739.05 W1 0.00 5866 6920.72 W2 0.00 2046 5029.50 W3 0.00 2628 5879.19 W4 0.00 4308 5022.74 W5 0.00 7396 5983.82 W6 0.00 9132 6467.88
- 10. PdomTSAr1.1-007723 (FC=2) Sample Expression Reads mapped Reads (adjusted) Q1 198.82 928 1005.53 Q2 445.48 1864 955.36 Q3 335.03 1330 961.89 Q4 267.42 1048 913.21 Q5 908.57 3988 960.82 Q6 114.54 458 1018.00 W1 125.65 714 842.38 W2 0.00 318 781.71 W3 78.41 426 953.02 W4 116.07 650 757.84 W5 161.56 1028 831.72 W6 147.01 1262 893.83
- 11. RSEM expected count 'expected_count' is the sum of the posterior probability of each read comes from this transcript over all reads. Because 1) each read aligning to this transcript has a probability of being generated from background noise; 2) RSEM may filter some alignable low quality reads, the sum of expected counts for all transcript are generally less than the total number of reads aligned.
- 12. Next (final) steps Look more into “expected count” Additional filtering? Publish!