Consensus Clustering - Revision history

Smith: /* Overview */

2014-01-24T20:39:46Z

‎Overview

2014-01-24T20:31:23Z

‎References - GenePattern

2014-01-24T20:28:15Z

‎References

2014-01-14T21:57:40Z

‎GenePattern Server Settings

2014-01-14T21:48:48Z

‎GenePattern Server Settings

2014-01-14T21:43:59Z

‎Results

2014-01-13T19:58:07Z

‎Overview

2013-11-27T00:00:13Z

2013-09-17T21:32:34Z

2013-08-09T21:48:45Z

‎Results

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 ==Overview==
-This component allows geWorkbench to run Consensus Clustering on a GenePattern server.  The user must supply the URL of an available GenePattern server.  All results are returned to geWorkbench, and the clustered arrays or markers are available as sets for further analysis.
+This component allows geWorkbench to run Consensus Clustering on a [http://www.broadinstitute.org/cancer/software/genepattern GenePattern] server.  The user must supply the URL of an available GenePattern server.  All results are returned to geWorkbench, and the clustered arrays or markers are available as sets for further analysis.
 As described in the GenePattern documentation, "Consensus clustering provides for a method to represent the consensus across multiple runs of a clustering algorithm and to assess the stability of the discovered clusters. To this end, perturbations of the original data are simulated by resampling techniques".

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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].
 * GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
 ==References - Consensus Clustering==

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 [[File:Consensus_clustering_output_files.png]]
-==References==
+==References - GenePattern==
 Monti S, Tamayo P, Mesirov J, and Golub T. Consensus Clustering: A resampling-based method for class discovery and visualization of gene expression microarray data (2003) Machine Learning Journal '''52'''(1-2):91-118.

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-* '''Protocol''' - http
+To run GenePattern components, a GenePattern account is required.
-* '''Host''' - enter the URL of an available GenePattern server.
-* '''Port''' - Enter the port number of the GenePattern server you are using.
+Pushing "'''Modify'''" brings up an editing box where any of the settings can be changed.
-* '''Username''' - enter a GenePattern username
-* '''Password''' - the GenePattern password for username, if required.
+* '''Protocol''' - HTTP or HTTPS, depending on the server being used.
 ==Results==

← Older revision		Revision as of 21:48, 14 January 2014
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−		+	* '''Protocol''' - http
		+	* '''Host''' - enter the URL of an available GenePattern server.
		+	* '''Port''' - Enter the port number of the GenePattern server you are using.
		+	* '''Username''' - enter a GenePattern username
		+	* '''Password''' - the GenePattern password for username, if required.

	==Results==		==Results==

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 * '''heat map size''' - point size of a consensus matrix's heat map (between 1 and 20)
 * '''cluster list name''' - name for new geWorkbench marker/array context in which to store clusters.  This should be changed to a name meaningful for your setup.
 ==Results==
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 [[File:Consensus_clustering_result_color_mosaic.png|{{ImageMaxWidth}}]]
 ==Access to Original Output Files==

← Older revision	Revision as of 21:32, 17 September 2013
(No difference)

← Older revision		Revision as of 21:48, 9 August 2013
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−	A special file browser is also provided, which can be activated by selecting the "Cluster Results" node under the parent data node in the Workspace. Any desired result file can be selected and exported to disk in its native format.	+	==Access to Original Output Files==
		+
		+	A special file browser is also provided, which can be activated by selecting the "Cluster Results" node under the parent data node in the Workspace. Any desired result file can be selected and exported to disk in its native format. The files returned include the clusters represented in the GenePattern GCT format, the cluster statistics files, and individual clusters.

	* '''Select''' - check the box for files to be saved to disk.		* '''Select''' - check the box for files to be saved to disk.