Showing posts from September, 2022

PCA, PCoA, and Tree Plot using NTSYSpc

This tutorial explains how to perform P rincipal C omponent A nalysis (PCA) and P rincipal C oordinate A nalysis (PCoA) of multivariate data using the NTSYSpc tool. NTSYSpc ( N umerical T axonomy and Multivariate Analysis SYS tem for p ersonal c omputer) is a simple and efficient statistical tool used to find patterns and display structures in multivariate data. The tool used in this tutorial is NTSYSpc v2.11a . In this tutorial, I have used a sample allelic data matrix (shown below). The matrix file consists of molecular weight size marker (rows) and sample/loci (columns). \[M_{mw,s}=\begin{bmatrix}0&0&1&1&0&0\\0&0&1&0&0&0\\0&0&1&1&0&0\\0&0&1&1&1&1\\1&1&1&0&0&0\\0&1&1&1&0&0\\0&0&1&1&1&1\\0&0&0&0&1&1\\1&0&0&0&0&0\\1&1&0&0&0&0\\1&1&0&0&0&0\\0&1&0&0&a