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Lecture

Principal Component Analysis: Understanding Data Structure

In courses (2)

MATH-474: Statistics for genomic data analysis

After a short introduction to basic molecular biology and genomic technologies, this course covers the most useful statistical concepts and methods for the analysis of genomic data. ...

MATH-493: Applied biostatistics

This course covers topics in applied biostatistics, with an emphasis on practical aspects of data analysis using R statistical software. Topics include types of studies and their design and analysis, high dimensional data analysis (genetic/genomic) and oth ...

Description

This lecture covers the concept of Principal Component Analysis (PCA) as a tool to reduce the dimensionality of data by creating linear combinations of variables. It explains how PCA aims to interpret the variance-covariance structure and how to determine the number of principal components to retain. The lecture also delves into the caution needed when interpreting PCA results, methods for assessing data quality using PCA, and the importance of controlling error rates in hypothesis testing.

Instructor

Darlene Goldstein

Official source

Related concepts (32)

Covariance matrix

In probability theory and statistics, a covariance matrix (also known as auto-covariance matrix, dispersion matrix, variance matrix, or variance–covariance matrix) is a square matrix giving the covariance between each pair of elements of a given random vector. Any covariance matrix is symmetric and positive semi-definite and its main diagonal contains variances (i.e., the covariance of each element with itself). Intuitively, the covariance matrix generalizes the notion of variance to multiple dimensions.

Statistical hypothesis testing

A statistical hypothesis test is a method of statistical inference used to decide whether the data at hand sufficiently support a particular hypothesis. Hypothesis testing allows us to make probabilistic statements about population parameters. While hypothesis testing was popularized early in the 20th century, early forms were used in the 1700s. The first use is credited to John Arbuthnot (1710), followed by Pierre-Simon Laplace (1770s), in analyzing the human sex ratio at birth; see .

Principal component analysis

Principal component analysis (PCA) is a popular technique for analyzing large datasets containing a high number of dimensions/features per observation, increasing the interpretability of data while preserving the maximum amount of information, and enabling the visualization of multidimensional data. Formally, PCA is a statistical technique for reducing the dimensionality of a dataset. This is accomplished by linearly transforming the data into a new coordinate system where (most of) the variation in the data can be described with fewer dimensions than the initial data.

Covariance

In probability theory and statistics, covariance is a measure of the joint variability of two random variables. If the greater values of one variable mainly correspond with the greater values of the other variable, and the same holds for the lesser values (that is, the variables tend to show similar behavior), the covariance is positive. In the opposite case, when the greater values of one variable mainly correspond to the lesser values of the other, (that is, the variables tend to show opposite behavior), the covariance is negative.

Sample mean and covariance

The sample mean (sample average) or empirical mean (empirical average), and the sample covariance or empirical covariance are statistics computed from a sample of data on one or more random variables. The sample mean is the average value (or mean value) of a sample of numbers taken from a larger population of numbers, where "population" indicates not number of people but the entirety of relevant data, whether collected or not. A sample of 40 companies' sales from the Fortune 500 might be used for convenience instead of looking at the population, all 500 companies' sales.

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