Introduction

If you’re interested in data analysis and interpretation, then this is the data science course for you. We start by learning the mathematical definition of distance and use this to motivate the use of the singular value decomposition (SVD) for dimension reduction and multi-dimensional scaling and its connection to principle component analysis. We will learn about the batch effect: the most challenging data analytical problem in genomics today and describe how the techniques can be used to detect and adjust for batch effects. Specifically, we will describe the principal component analysis and factor analysis and demonstrate how these concepts are applied to data visualization and data analysis of high-throughput experimental data.

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Finally, we give a brief introduction to machine learning and apply it to high-throughput data. We describe the general idea behind clustering analysis and descript K-means and hierarchical clustering and demonstrate how these are used in genomics and describe prediction algorithms such as k-nearest neighbors along with the concepts of training sets, test sets, error rates and cross-validation.

What you'll learn:

  • Mathematical Distance
  • Dimension Reduction
  • Singular Value Decomposition and Principal Component Analysis
  • Multiple Dimensional Scaling Plots
  • Factor Analysis
  • Dealing with Batch Effects
  • Clustering
  • Heatmaps
  • Basic Machine Learning Concepts

Given the diversity in educational background of our students we have divided the series into seven parts. You can take the entire series or individual courses that interest you. If you are a statistician you should consider skipping the first two or three courses, similarly, if you are biologists you should consider skipping some of the introductory biology lectures. Note that the statistics and programming aspects of the class ramp up in difficulty relatively quickly across the first three courses. By the third course will be teaching advanced statistical concepts such as hierarchical models and by the fourth advanced software engineering skills, such as parallel computing and reproducible research concepts.

The Data Analysis for Life Sciences courses are self-paced and include:

  1. Statistics and R for the Life Sciences
  2. Introduction to Linear Models and Matrix Algebra
  3. Statistical Inference and Modeling for High-throughput Experiments
  4. High-Dimensional Data Analysis
  5. Introduction to Bioconductor: annotation and analysis of genomes and genomic assays 
  6. High-performance computing for reproducible genomics
  7. Case studies in functional genomics

 

Meet The Faculty

Rafael Irizarry

Rafael Irizarry

Professor of Biostatistics, Harvard School of Public Health

Dr. Irizarry received his bachelor’s in mathematics in 1993 from the University of Puerto Rico and his Ph.D. in statistics in 1998 from the University of California, Berkeley. He joined the faculty of the Department of Biostatistics in the Bloomberg School of Public Health in 1998 and was promoted to Professor in 2007. He is now Professor of Biostatistics and Computational Biology at the Dana Farber Cancer Institute and a Professor of Biostatistics at the Harvard T.H. Chan School of Public Health. Dr. Irizarry has worked on the analysis and pre-processing of microarray, next-generation sequencing, and genomic data, and is currently interested translational work, developing diagnostic tools and discovering biomarkers. Dr. Irizarry is one of the founders of the Bioconductor Project, an open source and open development software project for the analysis of genomic data.

Michael Love

Michael Love

Postdoctoral Fellow, T.H. Chan School of Public Health

Michael Love is a postdoctoral fellow with Dr. Irizarry in the Department of Biostatistics at the Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health. Dr. Love received his bachelor’s in mathematics in 2005 from Stanford University, his master’s in statistics in 2010 from Stanford University, and his Ph.D. in Computational Biology in 2013 from the Freie Universität Berlin. Dr. Love uses statistical models to infer biologically meaningful patterns from high-throughput sequencing data, and develops open-source statistical software for the Bioconductor Project.

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