Marker Sets - Revision history

Smith: /* Marker Sets (Context) */

2014-04-23T19:58:57Z

‎Marker Sets (Context)

Smith: /* Lower Pane Controls */

2014-04-23T19:39:54Z

‎Lower Pane Controls

Smith: /* Marker Sets pulldown menu */

2014-04-23T19:38:02Z

‎Marker Sets pulldown menu

Smith at 20:23, 22 April 2014

2014-04-22T20:23:33Z

Smith: /* Sort Markers */

2014-01-21T22:27:36Z

‎Sort Markers

Smith: /* Sort Markers */

2014-01-21T22:26:43Z

‎Sort Markers

Smith: /* Sort Markers */

2014-01-21T22:24:20Z

‎Sort Markers

Smith: /* Right-click menu */

2014-01-21T22:23:53Z

‎Right-click menu

Smith: /* Combine */

2012-06-05T20:30:54Z

‎Combine

Smith: moved Data Subsets - Markers to Marker Sets

2012-03-13T18:43:33Z

moved Data Subsets - Markers to Marker Sets

@@ Line 112: / Line 112: @@
 ===Marker Sets (Context)===
 * '''Pulldown menu''' - A list of marker set contexts.  Each context can contain different sets of markers.  All components will make use of the currently selected context.  If an analysis returns a marker set as a result, it is returned to the current marker set context.  Different contexts can be used to organize markers at different levels of detail, or different types of analyses.
 * '''New''' - This button will create a new, empty marker set context.

@@ Line 113: / Line 113: @@
 ===Marker Sets (Context)===
 * '''Pulldown menu''' - A list of marker set contexts.  Each context can contain different sets of markers.  All components will make use of the currently selected context.  If an analysis returns a marker set as a result, it is returned to the current marker set context.  Different contexts can be used to organize markers at different levels of detail, or different types of analyses.
-* '''New''' - This button will create a new marker set context.
+* '''New''' - This button will create a new, empty marker set context.
+A popup will ask for a name for the new context:
@@ Line 126: / Line 123: @@
-The new list will appear in the menu, with only the default "Selection" set as a member.
+The new context will appear in the menu, with only the default "Selection" set as a member.

@@ Line 111: / Line 111: @@
 ==Lower Pane Controls==
-===Marker Sets pulldown menu===
+===Marker Sets (Context)===
-Select which named list of marker sets to display. Each list can contain a different arrangement of the markers into subsets.
+* '''Pulldown menu''' - A list of marker set contexts.  Each context can contain different sets of markers.  All components will make use of the currently selected context.  If an analysis returns a marker set as a result, it is returned to the current marker set context.  Different contexts can be used to organize markers at different levels of detail, or different types of analyses.
 ===New===

@@ Line 8: / Line 8: @@
 Sets of microarrays can be used to group arrays in a meaningful fashion for statistical analysis.  For example, two such phenotypes might be the diseased and normal states of a tissue from which samples have been taken.  geWorkbench uses the terms "Case" and "Control" to categorize these, but in biological setting the equivalent would be "Experimental" vs "Control".
-This chapter discusses the use of sets of markers.  Please see the chapter [[Data_Subsets_-_Arrays | Data Subsets - Arrays]] for a discussion of the use of Array sets.
+This chapter discusses the use of sets of markers.  Please see the chapter [[Array_Sets | Array_Sets]] for a discussion of the use of Array sets.
-The figure below shows the Markers component located below the Project Folders component in geWorkbench.  The Arrays component is located in the same space, under the adjacent tab.
+The figure below shows the Markers component located below the [[Workspace]] component in geWorkbench.  The [[Array_Sets|Arrays]] component is located in the same space, under the adjacent tab.
@@ Line 150: / Line 150: @@
 ====Activate====
-Activate the selected set (see explanation [[Data_Subsets_-_Markers#Activating_Sets_of_Markers_and_Arrays | above]]).  This will set the check-box in front of the set name to checked.
+Activate the selected set (see explanation [[Marker_Sets#Activating_Sets_of_Markers_and_Arrays | above]]).  This will set the check-box in front of the set name to checked.
 Activating a set can also be done directly by checking the check box before its name.
@@ Line 158: / Line 158: @@
 ====Deactivate====
-Deactivate the selected set (see explanation [[Data_Subsets_-_Markers#Activating_Sets_of_Markers_and_Arrays | above]]).  Deactivating a set can also be done directly by unchecking the check box before its name.
+Deactivate the selected set (see explanation [[Marker_Sets#Activating_Sets_of_Markers_and_Arrays | above]]).  Deactivating a set can also be done directly by unchecking the check box before its name.

@@ Line 102: / Line 102: @@
 ====Sort Markers====
 The list of markers can be sorted by:
 * '''gene name'''

@@ Line 105: / Line 105: @@
 * '''gene name'''
 * '''probeset id'''
-* '''into the original order'''
+* '''into the original order''' - the order of the markers as loaded from the original data file.
 ==Lower Pane Controls==

@@ Line 99: / Line 99: @@
 ====Clear Selection====
 Clear the contents of the default "Selection" marker set.
 ==Lower Pane Controls==

@@ Line 160: / Line 160: @@
 ====Combine====
-Combine the selected sets into a new set.  Methods are:
+Combine two or more selected sets into a new set.  Methods are:
 * '''Union''' - Include all markers that appear in one or more of the selected sets.
 * '''Intersection ''' - Include only markers that are present in each of the selected sets.

← Older revision	Revision as of 18:43, 13 March 2012
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