Principal Component Analysis (pca): A Complete Overview

Principal Component Analysis (pca): A Complete Overview


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  • Source: Microbioz India

  • Date: 13 Mar,2024

Principal Component Analysis (PCA) is a very useful tool that is widely used for dimensionality reduction and data visualization. It helps in finding patterns and relationships in data by turning high dimensional input into a lower dimensional form with important information being retained.

This is an all-inclusive guide to help you comprehend what PCA really means.

Introduction to PCA:

The number of variables in a dataset may be reduced using a statistical technique called PCA while retaining its main characteristics.

It does this by transforming the original variables into new ones known as principal components, which are used to reduce the dimensions of the data set. They are linear combinations of the original variables, and they possess orthogonality among them.

Key Concepts:

To carry out PCA we first compute eigenvalues and eigenvectors of the covariance matrix of our data.

  1. Covariance Matrix: Determines how much one variable depends on or co-varies with another variable
  2. Explained Variance: Each principal component captures some proportion of variance in the data so that PCA aims at having fewer components that capture most variation possible
  3. Scree Plot: A figure indicating explained variance for each principal component to know how many components should be preserved

Steps in PCA:

  1. Standardize the Data: The scale of this method is sensitive because it does not use unstandardized observation units which require having mean = 0 and standard deviation = 1 for correct functioning of pca model.
  2. Compute the Covariance Matrix: Find all covariance matrices based on preprocessed observation vectors.
  3. Calculate Eigenvalues and Eigenvectors: Calculate eigenvalues and eigenvectors for each covariance matrix obtained previously.
  4. Select Principal Components: Choose k largest eigenvalue-eigenvector pairs representing topk highest variance directions as principal components (PCs).
  5. Transform the Data: Project raw data onto PCs space selected above.

Also read:

Understanding the Mathematics Behind Principal Component Analysis(PCA)

Applications of PCA:

  1. Dimensionality Reduction: Retention of most information when reducing variables number
  2. Data Visualization: Looking at high-dimensional data in few dimensions
  3. Noise Reduction: Getting rid of noise and irrelevant attributes from data.
  4. Feature Extraction: Feature selection in data is done through pca instead

Interpreting Results:

  1. Eigenvalues: Large eigenvalues indicate that a principal component captures more variance from the original variable.
  2. Eigenvectors: They point out where the maximum variance lies in the dataset.
  3. Loading Scores: These are the coefficients that show how much each individual feature contributes to a principal component.
  4. Biplot: A scatter plot showing both observations and variables in PC space


  1. Data Scaling: To get meaningful results, PCA needs scaling of input values.
  2. Number of Components: Balance between dimension reduction and information loss should be considered with some limitation to retain only significant components will give meaning full insight.
  3. Interpretability: The meaning behind PCA components may not be directly tied back to what was used as input.

Extensions and Variants:

  1. Kernel PCA extends PCA to allow for non-linear dimensionality reduction using kernel functions.
  2. Sparse PCA incorporates sparseness constraints into unsupervised learning methods like Principal Component Analysis (PCA) which is useful when performing feature selection procedures or functions respectively
  3. Incremental PCA processes large datasets by batch so as not having all records calculated at once unlike classical approach which does everything together during fitting process with OLS, gradient descent etc methods can do only one pass over the whole training set;


Python NumPy, scikit-learn R, MATLAB and many others are among programming languages that have implemented this technique called PCA already

Resources for Learning PCA:

  1. Online courses, tutorials, textbooks about multivariate analysis including PCA,
  2. Practical examples and case studies,
  3. Open-source software/libraries with documentation/examples/tutorials on GitHub or other sites provide implementations/etc


Data analysis, machine learning, and statistics are among many fields where PCA can be used meaning it is versatile. It is good to try and learn what this technique is about that can aid in the analysis of high-dimensional data sets. The mastery of PCA comes with experiment and practical application which determines how one applies PCA in real life situations.

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