PCA Utilities

The PCA Utilities package provides small software routines for plotting PCA/OPLS scores and building dendrograms based on those scores. This page outlines how to install and use the pca-utils software.

Obtaining pca-utils

You can obtain the source code to pca-utils by clicking here.

Installing pca-utils

The PCA utilities are a set of command line open-source UNIX/Linux programs. The software is highly portable: provided your distribution has glibc, it should compile without incident. Once you have the source code, run these commands to install it:

cd /path/to/source/tarball
tar xf pca-utils-YYYYMMDD.tar.gz
cd pca-utils-YYYYMMDD/
make
sudo make install

By default, the programs install to /usr/bin, but you can easily change this by modifying the Makefile if you need to.

Plotting scores with ellipses

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Generating dendrograms

Two complementary methods exist for generating trees. The first uses Euclidean distances and bootstrapping statistics, while the second uses Mahalanobis distances and p-values. For datasets containing well-separated groups in scores space, the bootstrapping method will do fine. However, highly separation in overlapped data may be better quantified with p-values in many cases.

Using bootstrapping

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Using parameterizing

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Calculating p-values

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Calculating basic statistics

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Generating random datasets

FIXME