Array Sets - Revision history

Smith: /* Array/Phenotype Sets (Context) */

2014-04-23T19:56:53Z

‎Array/Phenotype Sets (Context)

Smith: /* Array/Phenotype Sets (Context) */

2014-04-23T19:56:24Z

‎Array/Phenotype Sets (Context)

Smith: /* Array Sets (Context) */

2014-04-23T19:49:10Z

‎Array Sets (Context)

Smith: /* Lower Pane Controls */

2014-04-23T19:48:22Z

‎Lower Pane Controls

Smith: /* Lower Pane Controls */

2014-04-23T19:47:20Z

‎Lower Pane Controls

Smith at 20:11, 22 April 2014

2014-04-22T20:11:01Z

Smith: /* Overview of Marker and Array Sets */

2013-10-16T21:29:31Z

‎Overview of Marker and Array Sets

Ut2102: /* Visual Properties */

2013-07-16T18:30:18Z

‎Visual Properties

Smith: moved Data Subsets - Arrays to Array Sets

2012-03-13T18:43:55Z

moved Data Subsets - Arrays to Array Sets

Smith: /* Working with multiple lists of array sets */

2012-02-23T21:36:52Z

‎Working with multiple lists of array sets

@@ Line 125: / Line 125: @@
 ===Array/Phenotype Sets (Context)===
 * '''Pulldown menu''' - A list of array set contexts.  Each context can contain different sets of arrays.  All components will make use of the currently selected context.  If an analysis returns an array set as a result, it is returned to the current array set context.  Different contexts can be used to organize arrays at different levels of detail, or different types of analyses.
 * '''New''' - This button will create a new, empty array set context.
 * '''Note''' - The [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench.29| Affymetrix Matrix File]] microarray data file format, native to geWorkbench, supports multiple such contexts of array sets being defined and saved.

← Older revision		Revision as of 19:56, 23 April 2014
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−	[[Image:~~Arrays_Create_New_List~~.png]]	+	[[Image:Arrays_Create_New_Context.png]]

@@ Line 124: / Line 124: @@
-===Array Sets (Context)===
+===Array/Phenotype Sets (Context)===
 * '''Pulldown menu''' - A list of array set contexts.  Each context can contain different sets of arrays.  All components will make use of the currently selected context.  If an analysis returns an array set as a result, it is returned to the current array set context.  Different contexts can be used to organize arrays at different levels of detail, or different types of analyses.
 * '''New''' - This button will create a new, empty array set context.
@@ Line 145: / Line 145: @@
 [[Image:Arrays_New_List_Created.png]]
 ===Load Set===

← Older revision		Revision as of 19:48, 23 April 2014
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	* '''Note''' - The [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench.29\| Affymetrix Matrix File]] microarray data file format, native to geWorkbench, supports multiple such contexts of array sets being defined and saved.		* '''Note''' - The [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench.29\| Affymetrix Matrix File]] microarray data file format, native to geWorkbench, supports multiple such contexts of array sets being defined and saved.
−
−	~~===New===~~
−	~~This button will create a new, empty context for array sets.~~

@@ Line 123: / Line 123: @@
 The lower pane of the Arrays/Phenotypes component has the following controls:
-===Array/Phenotype Sets pulldown menu===
-Select which named list of array sets to display. Each list can contain a different arrangement of the arrays into subsets.
+===Array Sets (Context)===
-* '''Note''' - The [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench.29| Affymetrix Matrix File]] microarray data file format, native to geWorkbench, supports multiple such lists of array sets being defined and saved.
+* '''Pulldown menu''' - A list of array set contexts.  Each context can contain different sets of arrays.  All components will make use of the currently selected context.  If an analysis returns an array set as a result, it is returned to the current array set context.  Different contexts can be used to organize arrays at different levels of detail, or different types of analyses.
 ===New===
-This button will create a new, empty list for array sets.
+This button will create a new, empty context for array sets.
@@ Line 134: / Line 137: @@
-A popup will ask for a name for the new list:
+A popup will ask for a name for the new context:
@@ Line 141: / Line 144: @@
-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 10: / Line 10: @@
 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 microarrays.  Please see the chapter [[Data_Subsets_-_Markers | Data Subsets - Markers]] for a discussion of the use of Marker sets.
+This chapter discusses the use of sets of microarrays.  Please see the chapter [[Marker_Sets]] for a discussion of the use of Marker sets.
-The figure below shows the Arrays/Phenotypes component located below the Workspace in geWorkbench.  The Markers component is located in the same space, under the adjacent tab.
+The figure below shows the Arrays/Phenotypes component located below the Workspace in geWorkbench.  The [[Marker_Sets| Markers]] component is located in the same space, under the adjacent tab.
@@ Line 22: / Line 22: @@
 ===Activating Sets of Markers and Arrays===
-In the Markers and the Arrays components, sets of markers and arrays can be defined by the user.  Such sets are also created as the outcome of various analysis methods.  Adjacent to each set in the graphical interface is a checkbox.  Checking this box '''activates''' the subset.
+In the [[Marker_Sets|Markers]] and the Arrays components, sets of markers and arrays can be defined by the user.  Such sets are also created as the outcome of various analysis methods.  Adjacent to each set in the graphical interface is a checkbox.  Checking this box '''activates''' the subset.
 * '''Activating''' a set restricts many geWorkbench components to using as input only the markers or arrays that are in one or more such activated sets.
 * '''Marker Sets'''
-** If no Marker set is active, all Markers are used.
+** If no marker set is active, all markers are used.
-** If at least one Marker set is activated, affected components will only use markers that are in activated sets.
+** If at least one marker set is activated, affected components will only use markers that are in activated sets.
 * '''Array Sets'''
 ** If no Array set is active, all Arrays are used.
 ** If at least one Array set is activated, affected components will only use arrays that are in activated sets.
-* '''Selection''' set - this is a special, default set.  One is present in both the Markers component and the Arrays component.  The "Selection" set has the following properties:
+* '''Selection''' set - this is a special, default set.  One is present in both the [[Marker_Sets|Markers]] component and the Arrays component.  The "Selection" set has the following properties:
 ** Double-clicking on a marker or array entry in the upper pane list will add that entry to the default "Selection" set.  Double-clicking the same entry again will remove it from the default set.
 ** The "Selection" set cannot be deleted.
@@ Line 171: / Line 171: @@
 ====Activate====
-Activate the selected set (see explanation [[Data_Subsets_-_Arrays#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 [[Array_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 182: / Line 182: @@
 ====Deactivate====
-Deactivate the selected set (see explanation [[Data_Subsets_-_Arrays#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 [[Array_Sets#Activating_Sets_of_Markers_and_Arrays | above]]).  Deactivating a set can also be done directly by unchecking the check box before its name.
 ====Delete====

← Older revision		Revision as of 21:29, 16 October 2013
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	This chapter discusses the use of sets of microarrays. Please see the chapter [[Data_Subsets_-_Markers \| Data Subsets - Markers]] for a discussion of the use of Marker sets.		This chapter discusses the use of sets of microarrays. Please see the chapter [[Data_Subsets_-_Markers \| Data Subsets - Markers]] for a discussion of the use of Marker sets.

−	The figure below shows the Arrays/Phenotypes component located below the ~~Project Folders component~~ in geWorkbench. The Markers component is located in the same space, under the adjacent tab.	+	The figure below shows the Arrays/Phenotypes component located below the Workspace in geWorkbench. The Markers component is located in the same space, under the adjacent tab.

@@ Line 227: / Line 227: @@
 After the visual properties of the "GC B-cell" set have been altered, we can view their appearance in, for example, the Scatter Plot component.  Here we have activated both the "GC B-cell" set and the "non-GC B-cell" set.  The former now uses the green plus signs, whereas the later uses a system assigned default color and shape.
-[[Image:Arrays_Change_visual_properties_scatter_plot.png]]
+[[Image:Arrays_Change_visual_properties_scatter_plot.png|{{ImageMaxWidth}}]]
 ====Classification====

← Older revision	Revision as of 18:43, 13 March 2012
(No difference)

← Older revision		Revision as of 21:36, 23 February 2012
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	If instead we choose the list "Source - short", a different division into subsets of the same arrays is seen:		If instead we choose the list "Source - short", a different division into subsets of the same arrays is seen:

−	[[Image:~~Arrays_ListOfSets_CellLine~~.png]]	+	[[Image:Arrays_Set_Short.png]]