PCA Utilities - Revision history

Mjeppesen at 06:33, 20 January 2022

2022-01-20T06:33:10Z

← Older revision		Revision as of 06:33, 20 January 2022
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	No, you read that right. [[Media:Beatles.txt \|You can download the list file generated by a single run of this command.]]		No, you read that right. [[Media:Beatles.txt \|You can download the list file generated by a single run of this command.]]

	~~[[category:Data_Processing_and_Analysis]]~~

	= "Wait, I'm still confused" =		= "Wait, I'm still confused" =
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	man pca-dendrogram		man pca-dendrogram

	~~[[category:Protocols]]~~
	~~[[category:Metabolomics]]~~
	[[category:Data_Processing_and_Analysis]]		[[category:Data_Processing_and_Analysis]]

2022-01-20T06:32:12Z

Introductions

← Older revision		Revision as of 06:32, 20 January 2022
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	= Introductions =		= Introductions =
			Modeling algorithms like PCA, PLS and OPLS project a set of K-variate observations into a low-dimensional "latent" space. In this space, the original observations are represented by points (scores), and distances between the points are related to the original distances between the high-dimensional observations.

			Some obvious questions that arise when discriminating between classes are:

			#How far apart are classes in scores space?
			#Are the scores-space separations significant?
			#Is there a higher pattern to the separations?
			The pca-utils project provides a set of executables that answer these questions. The executables allow for generating dendrograms, distance matrices, class ellipses and ellipsoids based on a set of scores.

	== Obtaining ''pca-utils'' ==		== Obtaining ''pca-utils'' ==
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	pca-rand -L Ringo -u '(-1,-1)' -v '(2,2)' -r 0 -n 15) > ''list.txt''		pca-rand -L Ringo -u '(-1,-1)' -v '(2,2)' -r 0 -n 15) > ''list.txt''

	No, you read that right. You can download the list file generated by a single run of this command ~~here:~~ [[~~File~~:~~Beatles.txt~~]].		No, you read that right. [[Media:Beatles.txt \|You can download the list file generated by a single run of this command.]]

			[[category:Data_Processing_and_Analysis]]

	= "Wait, I'm still confused" =		= "Wait, I'm still confused" =

2021-09-11T05:02:37Z

Added to Category

← Older revision		Revision as of 05:02, 11 September 2021
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	[[category:Protocols]]		[[category:Protocols]]
	[[category:Metabolomics]]		[[category:Metabolomics]]
			[[category:Data_Processing_and_Analysis]]

2015-07-13T18:40:54Z

← Older revision		Revision as of 18:40, 13 July 2015
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	== Obtaining ''pca-utils'' ==		== Obtaining ''pca-utils'' ==
	You can obtain the source code to ''pca-utils'' ~~by clicking~~ [http://~~bionmr~~.~~unl.edu~~/pca-utils~~.php here~~].		You can obtain the source code to ''pca-utils'' on its [http://github.com/geekysuavo/pca-utils GitHub page].

	== Installing ''pca-utils'' ==		== 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:		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~~		git clone git://github.com/geekysuavo/pca-utils.git
	~~tar xf~~ pca-utils~~-YYYYMMDD.tar~~.gz		cd pca-utils
	cd pca-utils~~-YYYYMMDD/~~
	make		make
	sudo make install		sudo make install

2013-08-06T17:03:04Z

← Older revision		Revision as of 17:03, 6 August 2013
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	pca-overlap -i ''list.txt''		pca-overlap -i ''list.txt''

			== Calculating distances ==
			Similar to calculating p-values, raw distances may be extracted using the following command:

			pca-distances -i ''list.txt''

			Other distance metrics may be supplied using the '''-m''' flag. For example, you can generate a [[wikipedia:Mahalanobis distance\|Mahalanobis distance]] matrix like so:

			pca-distances -m MAH -i ''list.txt''

	== Calculating basic statistics ==		== Calculating basic statistics ==

2012-10-02T23:33:42Z

Obtaining pca-utils

← Older revision		Revision as of 23:33, 2 October 2012
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	== Obtaining ''pca-utils'' ==		== Obtaining ''pca-utils'' ==
	You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu~~/files~~/pca-utils~~/pca-utils-20120820.tar~~.gz here].		You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/pca-utils.php here].

	== Installing ''pca-utils'' ==		== Installing ''pca-utils'' ==

2012-08-21T07:05:47Z

"Wait, I'm still confused"

← Older revision		Revision as of 07:05, 21 August 2012
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	= "Wait, I'm still confused" =		= "Wait, I'm still confused" =
	Remember that every command in the ''pca-utils'' package has a help message. Just run the command that you need information on with the ''--help'' flag to get a nice message on how to use that command.		Remember that every command in the ''pca-utils'' package has a help message. Just run the command that you need information on with the ''--help'' flag to get a nice message on how to use that command. You can also find manual pages for each command, e.g.:

			man pca-dendrogram

	[[category:Protocols]]		[[category:Protocols]]
	[[category:Metabolomics]]		[[category:Metabolomics]]

2012-08-21T03:07:42Z

Obtaining pca-utils

← Older revision		Revision as of 03:07, 21 August 2012
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	== Obtaining ''pca-utils'' ==		== Obtaining ''pca-utils'' ==
	You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/files/pca-utils/pca-utils-~~20120809~~.tar.gz here].		You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/files/pca-utils/pca-utils-20120820.tar.gz here].

	== Installing ''pca-utils'' ==		== Installing ''pca-utils'' ==

2012-08-15T02:22:44Z

Plotting 3D scores with ellipsoids

@@ Line 40: / Line 40: @@
   gnuplot
   '''gnuplot>''' load 'plotscript.plt'
 == Generating dendrograms ==

2012-08-10T07:21:15Z

Obtaining pca-utils

← Older revision		Revision as of 07:21, 10 August 2012
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	== Obtaining ''pca-utils'' ==		== Obtaining ''pca-utils'' ==
	You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/files/pca-utils/pca-utils-~~20120807~~.tar.gz here].		You can obtain the source code to ''pca-utils'' by clicking [http://bionmr.unl.edu/files/pca-utils/pca-utils-20120809.tar.gz here].

	== Installing ''pca-utils'' ==		== Installing ''pca-utils'' ==