Volcano Plot - Revision history

Smith at 00:29, 23 January 2014

2014-01-23T00:29:49Z

2013-07-16T19:50:12Z

‎Overview

2012-07-11T22:11:00Z

2012-07-11T19:30:40Z

‎Export Data

2012-07-11T19:22:01Z

‎Export Data

2012-07-11T19:20:04Z

2012-07-11T16:32:39Z

‎Fold Change

2012-07-11T16:28:37Z

‎Fold Change

2011-12-21T00:08:59Z

‎Fold Change

2011-09-09T16:08:47Z

‎Color scheme

@@ Line 10: / Line 10: @@
 Markers for which no valid fold-change value could be calculated (e.g. for the case of linear data the average of the case or control values was negative) are omitted from the Volcano Plot.  However, all such markers are included if the data is exported to file.
-The Volcano Plot viewer is only available when a t-test result is selected in the Project Folders component.
+The Volcano Plot viewer is only available when a t-test result is selected in the [[Workspace]].
 ==Fold Change==

@@ Line 3: / Line 3: @@
 ==Overview==
-[[Image:Volcano_plot.png]]
+[[Image:Volcano_plot.png|{{ImageMaxWidth}}]]
@@ Line 11: / Line 11: @@
 The Volcano Plot viewer is only available when a t-test result is selected in the Project Folders component.
 ==Fold Change==

← Older revision		Revision as of 19:30, 11 July 2012
Line 27:		Line 27:
	The column headers are: Probe Set Name, Gene Name, p-Value, Fold Change (log2).		The column headers are: Probe Set Name, Gene Name, p-Value, Fold Change (log2).

−	Markers found significant in the t-test are included in the export file ~~even if they did not have a fold-change value calculated, and hence do~~ not ~~appear~~ in the Volcano Plot.	+	Markers found significant in the t-test, but for which a fold change value could not be calculated, are included in the export file as "N/A". They are not displayed in the Volcano Plot.

← Older revision		Revision as of 19:22, 11 July 2012
Line 27:		Line 27:
	The column headers are: Probe Set Name, Gene Name, p-Value, Fold Change (log2).		The column headers are: Probe Set Name, Gene Name, p-Value, Fold Change (log2).

−	~~Even markers for which~~ a fold-change value ~~was not~~ calculated, and ~~which are~~ not ~~displayed~~ in the Volcano Plot~~, are included in the export file~~.	+	Markers found significant in the t-test are included in the export file even if they did not have a fold-change value calculated, and hence do not appear in the Volcano Plot.

@@ Line 5: / Line 5: @@
-The Volcano Plot visualizer graphs the log2 fold change for each marker against the -log10 of the P-value.
+The Volcano Plot graphically depicts the results of the t-test for differential expression.  It includes only markers which exceeded the threshold for significance in the t-test.  The log2 fold change for each marker is plotted against the -log10 of the P-value.
 ==Fold Change==
@@ Line 20: / Line 23: @@
 ==Export Data==
-The data depicted in the volcano plot is exported to a CSV format file.  The column headers are: Probe Set Name, Gene Name, p-Value, Fold Change.
+Exports data for all markers in the t-test result node to a CSV format file.

@@ Line 12: / Line 12: @@
 The method used to calculate fold change depends on whether the data was marked as log2 transformed or not during the t-test using the "Data is log2 transformed" box.
-* "Data is log2 transformed" box '''was not''' checked: the fold change is calculated, for each marker, as the Log2 transform of the average expression in the Case set divided by the average expression in the control set, that is, Log2(Avg(cases)/Avg(controls)) or Log2(Avg(cases)) - Log2(Avg(controls)).  (Difference of logs of averaged values).
+* '''Linear data''' ("Data is log2 transformed" box '''was not''' checked): the fold change is calculated, for each marker, as the Log2 transform of the average expression in the Case set divided by the average expression in the control set, that is, Log2(Avg(cases)/Avg(controls)) or Log2(Avg(cases)) - Log2(Avg(controls)).  (Difference of logs of averaged values).
-* "Data is log2 transformed" box '''was''' checked: In this case, for each marker, the average of the log case values minus the average of the log control values is calculated, that is, Avg(cases) - Avg(controls).  (Difference of averaged log values).
+* '''Log2 transformed data''' ("Data is log2 transformed" box '''was''' checked): In this case, for each marker, the average of the (log) case values minus the average of the (log) control values is calculated, that is, Avg(cases) - Avg(controls).  (Difference of averaged log values).
 ==Color scheme==

@@ Line 12: / Line 12: @@
 The method used to calculate fold change depends on whether the data was marked as log2 transformed or not during the t-test using the "Data is log2 transformed" box.
-* "Data is log2 transformed" box '''was not''' checked: the fold change is calculated, for each marker, as the average expression in the Case set divided by the average expression in the control set.  The Log2 transform of these values are displayed, that is, Log2(Avg(cases)/Avg(controls)) or Log2(Avg(cases)) - Log2(Avg(controls)).
+* "Data is log2 transformed" box '''was not''' checked: the fold change is calculated, for each marker, as the average expression in the Case set divided by the average expression in the control set.  The Log2 transform of these values are displayed, that is, Log2(Avg(cases)/Avg(controls)) or Log2(Avg(cases)) - Log2(Avg(controls)).  (Difference of logs of averaged values).
-* "Data is log2 transformed" box '''was''' checked: In this case, for each marker, the average of the log2 case values minus the average of the log2 control values is displayed, that is, Avg(log2(cases)) - Avg(log2(controls)).
+* "Data is log2 transformed" box '''was''' checked: In this case, for each marker, the average of the log2 case values minus the average of the log2 control values is displayed, that is, Avg(log2(cases)) - Avg(log2(controls)).  (Difference of averaged log values).
 ==Color scheme==