Microarray Dataset Viewers - Revision history

Smith: /* Expression Profiles */

2015-01-27T21:24:21Z

‎Expression Profiles

Smith: /* Outline */

2014-04-23T18:23:27Z

‎Outline

Smith: /* Expression Profiles */

2014-04-23T18:20:55Z

‎Expression Profiles

Smith: /* Expression Profiles */

2014-04-23T18:17:39Z

‎Expression Profiles

Smith: moved Viewing a Microarray Dataset to Microarray Dataset Viewers

2014-04-23T17:56:38Z

moved Viewing a Microarray Dataset to Microarray Dataset Viewers

Smith: /* Viewing a dataset */

2014-04-23T17:53:59Z

‎Viewing a dataset

Smith: /* Scatter Plot */

2014-04-23T17:53:24Z

‎Scatter Plot

Smith: /* Scatter Plot */

2014-04-23T17:51:02Z

‎Scatter Plot

Smith at 20:33, 22 April 2014

2014-04-22T20:33:56Z

Smith: /* Microarray Viewer */

2013-10-16T21:34:22Z

‎Microarray Viewer

@@ Line 85: / Line 85: @@
 ===Expression Profiles===
-For each actived marker, a line showing the expression value vs array is graphed.   Each marker is displayed with a separate color line.
+For each activated marker, a line showing the expression value vs array is graphed.   Each marker is displayed with a separate color line.
 * '''Plot'''' - The plot button must be pushed to draw the display.
-* '''Markers''' - If one or more marker sets have been activated, the number of markers is shown.
+* '''Markers''' - The number of markers is shown.
 * [[Image:Light_bulb_hover_icon.png]] - '''Hover-text detail on/off''' - Switch on or off the hover text detail on chart points.  When active, the identity of the marker and array at any point can be seen by placing the mouse over a point on the graph.  A hover text (shown in figure) will appear.

@@ Line 15: / Line 15: @@
 * Expression Profiles
 * Scatter Plot
 The options for several of the components are set from the application toolbar [[Menu_Bar#Preferences | Preferences]] menu, which will also be explained.
 ==Overview==

@@ Line 89: / Line 89: @@
 * '''Plot'''' - The plot button must be pushed to draw the display.
 * '''Markers''' - If one or more marker sets have been activated, the number of markers is shown.
-* '''Hover-text detail''' - The identity of the marker and array at any point can be seen by placing the mouse over a point on the graph.  A hover text (shown in figure) will appear.
+* [[Image:Light_bulb_hover_icon.png]] - '''Hover-text detail on/off''' - Switch on or off the hover text detail on chart points.  When active, the identity of the marker and array at any point can be seen by placing the mouse over a point on the graph.  A hover text (shown in figure) will appear.
 [[Image:Expression_Profiles.png]]

@@ Line 85: / Line 85: @@
 ===Expression Profiles===
-For each active marker (default is all), a line showing the expression value vs array is graphed.   Each marker is displayed with a separate color line.  The '''Plot''' button must be pushed to draw the display.  If a subset of markers has been activated, the number active is shown adjacent to the '''Markers''' label.  Right-click options are shown.
+For each actived marker, a line showing the expression value vs array is graphed.   Each marker is displayed with a separate color line.
-[[Image:T_Expression_Profiles.png]]
+[[Image:Expression_Profiles.png]]
 ===Scatter Plot===

← Older revision		Revision as of 17:53, 23 April 2014
Line 114:		Line 114:
	# In the Visualization Area at the top-right section of the interface, select any viewer described above, for example the '''Microarray Viewer''' component.		# In the Visualization Area at the top-right section of the interface, select any viewer described above, for example the '''Microarray Viewer''' component.
	# When no marker or array sets are activated, all markers or arrays, respectively, will be used.		# When no marker or array sets are activated, all markers or arrays, respectively, will be used.
−
−
−	~~[[Image: Allm.png]]~~

← Older revision	Revision as of 17:56, 23 April 2014
(No difference)

@@ Line 95: / Line 95: @@
 A pairwise (''array vs. array and marker vs. marker'') comparison and plotting of expression values.  The first array or marker selected serves as the x-axis reference, shown with a dark background; this can also be set by right-clicking and selecting the x-axis as shown).  Subsequent choices are plotted against this reference. Up to six graphs can be displayed. Right-click options are shown in the second picture.
-For two arrays, plot markers.  A single marker set "All" is activated.
+For two arrays, plot markers.  No [[Marker_Sets|marker set]] is activated so "All" is the label in the key.
@@ Line 101: / Line 101: @@
-For two markers, plot activated arrays.  Each activated array set is shown in a different color.
+For two markers, plot activated arrays.  Each [[Array_Sets|activated array set]] is shown in a different color.

@@ Line 93: / Line 93: @@
 ===Scatter Plot===
-A pairwise (''array vs. array and marker vs. marker'') comparison and plotting of expression values.  The first marker selected serves as the x-axis reference, shown with a dark background; this can also be set by right-clicking and selecting the x-axis marker as shown).  Subsequent arrays selected are plotted against this reference in different sub-images. Up to six sub-images can be created. Right-click options are shown in the second picture.
+A pairwise (''array vs. array and marker vs. marker'') comparison and plotting of expression values.  The first array or marker selected serves as the x-axis reference, shown with a dark background; this can also be set by right-clicking and selecting the x-axis as shown).  Subsequent choices are plotted against this reference. Up to six graphs can be displayed. Right-click options are shown in the second picture.
 ==Preparation==

@@ Line 6: / Line 6: @@
 ==Outline==
-In this section, various tools for visualizing microarray expression data will be introduced.  Available options for each component will be depicted.
+In this section, various tools for visualizing microarray expression data will be introduced.  These components will be available whenever a microarray dataset is selected in the [[Workspace]].  Available options for each component will be depicted.
 The visualizers displayed here are:
@@ Line 16: / Line 16: @@
 * Scatter Plot
-The options for several of the components are set from the application toolbar preferences menu, which will also be explained.
+The options for several of the components are set from the application toolbar [[Menu_Bar#Preferences | Preferences]] menu, which will also be explained.
 ==Overview==
-Visualization tools provide a view of the microarray datasets under investigation and can be used e.g. for ascertaining the quality of the data. Activating marker and array/phenotype sets ([[Tutorial - Data Subsets]]) can be used to restrict the number of markers/arrays displayed. The images created can be saved and exported. A more detailed description of how to manipulate visualization components is given in the online help.
+Visualization tools provide a view of the microarray datasets under investigation and can be used e.g. for ascertaining the quality of the data. Activating [[Marker_Sets|marker]] and [[Array_Sets|array/phenotype]] sets  can be used to restrict the number of markers/arrays displayed. The images created can be saved and exported. A more detailed description of how to manipulate visualization components is given in the online help.
@@ Line 48: / Line 48: @@
 * '''Decimal Places''' - choose how many places after the decimal to display.  Numbers are rounded to the specified precision.
-* '''Export''' - Exports the displayed data to a tab-delimited spreadsheet format file.  Note that the tabular viewer respects activated marker and array sets.  If marker or array sets in the Markers/Arrays component have been activated, only those markers and/or arrays in the activated sets will be written to the file.  This provides an easy way to export a subset of the data.
+* '''Export''' - Exports the displayed data to a tab-delimited spreadsheet format file.  Note that the tabular viewer respects activated marker and array sets.  If marker or array sets in the [[Marker_Sets|Markers]]/[[Array_Sets|Arrays]] component have been activated, only those markers and/or arrays in the activated sets will be written to the file.  This provides an easy way to export a subset of the data.
 ** Note - in the exported file, the format choices above are not preserved, and all significant digits are always written.
@@ Line 105: / Line 105: @@
 ==Viewing a dataset==
-#  In the View Area at the top-right section of the interface, select any viewer described above, for example the '''Microarray Viewer''' component.
+#  In the Visualization Area at the top-right section of the interface, select any viewer described above, for example the '''Microarray Viewer''' component.
-#  On many of the components, the '''All Markers''' and '''All Arrays''' checkboxes can be used to override the effects of activated sets, should they be in use.  When no sets are activated, all markers or arrays will be used.
+#  When no marker or array sets are activated, all markers or arrays, respectively, will be used.
 [[Image: Allm.png]]

@@ Line 26: / Line 26: @@
 ===Microarray Viewer===
-Used to inspect data from each separate microarray using the Array scroll bar. Note that the markers (probes or probesets) are displayed in the order they appear in the dataset, and the image is not a physical representation of the microarray layout.  The image can be saved into the '''Project Folders''' component under its parent dataset by right-clicking and selecting '''Save Image'''.
+Used to inspect data from each separate microarray using the Array scroll bar. Note that the markers (probes or probesets) are displayed in the order they appear in the dataset, and the image is not a physical representation of the microarray layout.  The image can be saved into the [[Workspace|Workspace]] under its parent dataset by right-clicking and selecting '''Save Image'''.
 The viewing preference shown here is the "relative" display mode.  See [[Menu_Bar#Preferences | Preferences]] for switching between relative and absolute display modes.