Classification - Revision history

Smith: /* References - GenePattern */

2014-01-24T20:31:06Z

‎References - GenePattern

2014-01-24T20:26:57Z

‎References - GenePattern

2014-01-24T20:26:21Z

‎References - GenePattern

2014-01-24T20:23:39Z

‎WV Classifier Parameters

2014-01-24T20:23:21Z

‎Example - Weighted Voting (WV)

2014-01-24T20:22:59Z

‎KNN Classifier Parameters

2014-01-24T20:22:41Z

‎Running the classification

2014-01-24T20:21:46Z

‎References - KNN

2014-01-24T20:18:30Z

‎Overview

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‎Outline

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 ==References - GenePattern==
-Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
+* Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].

@@ Line 180: / Line 180: @@
 ==References - GenePattern==
-Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [(http://www.ncbi.nlm.nih.gov/pubmed/16642009 PubMed 16642009)]
+Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [http://www.ncbi.nlm.nih.gov/pubmed/16642009 (PubMed 16642009)]
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].

@@ Line 180: / Line 180: @@
 ==References - GenePattern==
-Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500.
+Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500. [(http://www.ncbi.nlm.nih.gov/pubmed/16642009 PubMed 16642009)]
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
 ==References - KNN==

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 ===WV Classifier Parameters===
 * '''num features''' - number of signal-to-noise selected features if "feature filename" is not specified
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 * '''median''' - whether median should be used by "feature selection statistic" (optional)
 * '''feature filename''' - list of features to use for prediction (overrides feature selection parameters)
 ===Test Classifier Accuracy===

← Older revision		Revision as of 20:23, 24 January 2014
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	For the Weighted Voting example we will use the same data setup as described above for KNN. The server settings are also the same.		For the Weighted Voting example we will use the same data setup as described above for KNN. The server settings are also the same.
−
−
−	~~[[Image:WV_Analysis_Parameters.png\|{{ImageMaxWidth}}]]~~
−

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 ===KNN Classifier Parameters===
 * '''num features''' - number of signal-to-noise selected features if "feature filename" is not specified
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 ** Cosine
 ** Euclidean
 ===WV Classifier Parameters===

← Older revision		Revision as of 20:22, 24 January 2014
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−	On the parameters tab, adjust the parameters, or use the default values as ~~shown~~ in ~~the figure below.~~	+	* On the parameters tab, adjust the parameters, or use the default values as used in this example.
−
−
−	~~[[Image:KNN_Analysis_Parameters~~.~~png\|{{ImageMaxWidth}}]]~~
−

	* The first step is generation of the classifier and cross-validation. Click the "Test via Cross-Validation" button.		* The first step is generation of the classifier and cross-validation. Click the "Test via Cross-Validation" button.

← Older revision		Revision as of 20:21, 24 January 2014
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	[[Image:GP_KNN_and_WV_Class_Predictions.png]]		[[Image:GP_KNN_and_WV_Class_Predictions.png]]
		+
		+	==References - GenePattern==
		+	Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500.
		+
		+	* GenePattern [http://www.broadinstitute.org/cancer/software/genepattern website].
		+
		+	* GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
		+
		+

	==References - KNN==		==References - KNN==

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-At present, interfaces to three GenePattern classification algorithms have been implemented in geWorkbench.  These are:
+At present, geWorkbench provides interfaces to three GenePattern classification algorithms available on [http://www.broadinstitute.org/cancer/software/genepattern GenePattern] servers:
 * WV Classifier (Weighted-Voting)
 * KNN Classifier (K-Nearest Neighbors)

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 This tutorial contains
-# an overview describing two classification algorithms which run on a [http://www.broadinstitute.org/cancer/software/genepattern GenePattern] server
+# an overview describing two classification algorithms which run on a [http://www.broadinstitute.org/cancer/software/genepattern GenePattern] server, and that are available through geWorkbench: (i) K-Nearest Neighbors (KNN), and (ii) Weighted Voting,
 # a detailed example of setting up and running a KNN classification,
 # an similar example of running the Weighted Voting classification.