K-Means Clustering - Revision history

Smith at 16:57, 22 April 2014

2014-04-22T16:57:47Z

2014-01-24T20:30:36Z

‎References

2014-01-14T21:58:28Z

‎GenePattern Server Settings

2014-01-14T21:49:31Z

‎GenePattern Server Settings

2014-01-14T21:44:49Z

‎Results Viewer

2014-01-14T18:56:48Z

‎Parameters

2014-01-13T21:40:50Z

2014-01-13T21:34:44Z

‎Parameters

2014-01-13T21:32:11Z

‎K-Means "SOM" Cluster Viewer

2014-01-13T21:29:51Z

‎K-Means SOM Cluster Viewer

@@ Line 12: / Line 12: @@
 The K-Means clustering analysis and viewer components must be loaded in the [[Component_Configuration_Manager|Component_Configuration_Manager]]
-A gene expression dataset must be loaded in the Workspace.
+A gene expression dataset must be loaded in the [[Workspace|Workspace]].
 ==Parameters==
@@ Line 75: / Line 75: @@
 The two columns (if the clustering dimension "Genes" was chosen during analysis) are:
 * '''ProbeSetID''' - the probeset name in the dataset
-* '''Gene Symbol''' - the gene symbol for the probset, if an annotation file was loaded in the Workspace.
+* '''Gene Symbol''' - the gene symbol for the probset, if an annotation file was loaded in the [[Workspace|Workspace]].
-* '''Annotation''' - Annotation for each probeset, if an annotation file was loaded in the Workspace.
+* '''Annotation''' - Annotation for each probeset, if an annotation file was loaded in the [[Workspace|Workspace]].

@@ Line 112: / Line 112: @@
 The K-Means clustering component is found in the "gpmodule_v3_0" package in the geWorkbench component source tree.
-==References==
+==References - GenePattern==
 * J. B. MacQueen (1967) Some Methods for classification and Analysis of Multivariate Observations. Proceedings of 5th Berkeley Symposium on Mathematical Statistics and Probability, Berkeley, University of California Press, 1:281-297

@@ Line 34: / Line 34: @@
-* '''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 Viewer==

← Older revision		Revision as of 21:49, 14 January 2014
Line 34:		Line 34:


−		+	* '''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 Viewer==		==Results Viewer==

@@ Line 25: / Line 25: @@
 * '''Distance Metric'''
 ** Euclidean - the only option offered.
 ==Results Viewer==

@@ Line 15: / Line 15: @@
 ==Parameters==
 * '''Number of Clusters''' - This is the number ''k'' of clusters in which to group the data.
 * '''Cluster by'''

← Older revision		Revision as of 21:32, 13 January 2014
Line 75:		Line 75:

	For each displayed cluster, the horizontal axis represents the individual arrays. The colored lines represent each probeset. The vertical axis is the expression value.		For each displayed cluster, the horizontal axis represents the individual arrays. The colored lines represent each probeset. The vertical axis is the expression value.
		+
		+	Please see the tutorial for the [[SOM#SOM_Clusters_Viewer\| SOM Cluster Viewer]] for details of graphing options.

@@ Line 71: / Line 71: @@
 [[Image:KMeans_Marker_Analysis.png]]
-==K-Means SOM Cluster Viewer==
+==K-Means "SOM" Cluster Viewer==
 When the cluster dimension is "Genes", the clusters are displayed using the SOM cluster component.  Note - the clusters are still the K-Means clusters, just displayed using the SOM Viewer to allow simultaneous display of each cluster.
@@ Line 83: / Line 83: @@
-KMeans_Show_Selected.png
+[[Image:KMeans_Show_Selected.png]]
 ==Technical Note==