GeWorkbench-web/T-Test - Revision history

Smith: moved T-Test web to GeWorkbench-web/T-Test

2015-04-27T18:01:04Z

2015-03-27T22:32:17Z

2015-03-13T21:08:35Z

‎Volcano Plot Visualizer

2015-03-13T21:05:40Z

‎Export

2015-03-13T21:02:57Z

‎Hover text

2015-03-13T21:01:53Z

‎Volcano Plot Visualizer

2015-03-13T20:57:08Z

‎Volcano Plot Visualizer

2015-03-13T20:34:55Z

‎t-Test Results

2015-03-13T20:08:54Z

‎Example

2015-03-13T20:04:40Z

‎Example

← Older revision		Revision as of 22:32, 27 March 2015
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−	{{~~TutorialsTopNav~~}}	+	{{Template:GeWorkbench-webTutorialsTopNav}}

← Older revision		Revision as of 21:08, 13 March 2015
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	The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.		The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.
		+
		+
		+	===Color scheme===
		+	The lower 2/3 of the absolute values of the (fold change) * (significance) are colored in shades from light blue (lowest values) to dark blue (highest values). The highest 1/3 of such values are colored from dark blue (lowest values) to red (highest values).
		+
		+	* '''Note''' - the shading from light-blue to dark-blue is not currently working!
		+

	===Hover text===		===Hover text===

← Older revision		Revision as of 21:05, 13 March 2015
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	* p-Value		* p-Value
	* Fold Change (Log2) - As calculated using one of the two methods described above.		* Fold Change (Log2) - As calculated using one of the two methods described above.
		+
		+
		+	===Zoom and Reset Zoom===
		+	* ''Zoom action'' - The graph can be zoomed-in by left-clicking on the graph and dragging the mouse to select the zoom region.
		+
		+	* '''Reset Zoom''' - will return the plot to its original view.

@@ Line 142: / Line 142: @@
 [[Image:T-Test_web_volcano_plot_hover.png]]
-Hovering the cursor over a particular data point will bring up a hover text displaying the marker name and its plot coordinates, the log2 fold change value and the -log10(p-value).
+Hovering the cursor over a particular data point will highlight it as a larger blue circle and bring up a hover text displaying the marker name and its plot coordinates, the log2 fold change value and the -log10(p-value).
 ===Export===

← Older revision		Revision as of 21:01, 13 March 2015
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	The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.		The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.
		+
		+	===Hover text===
		+
		+	[[Image:T-Test_web_volcano_plot_hover.png]]
		+
		+	Hovering the cursor over a particular data point will bring up a hover text displaying the marker name and its plot coordinates, the log2 fold change value and the -log10(p-value).
		+

	===Export===		===Export===

← Older revision	Revision as of 18:01, 27 April 2015
(No difference)

← Older revision		Revision as of 20:57, 13 March 2015
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	The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.		The fold change is calculate as described in the previous section based on whether the data was log2 transformed or not.
		+
		+	===Export===
		+
		+	[[Image:Volcano_Plot_web_Export_Menu.png]]
		+
		+	There are three export options:
		+	* Plot - Open a SVG file in a new browser window.
		+	* Data as Excel - Export the data to an Excel format file.
		+	* Data as CSV - Export the data to a CSV format file.
		+
		+	For the Excel and CSV format files, the following colums will be contained in the file:
		+
		+	* Probe Set Name
		+	* Gene Name (from Annotation file)
		+	* p-Value
		+	* Fold Change (Log2) - As calculated using one of the two methods described above.

← Older revision		Revision as of 20:34, 13 March 2015
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	The fold change is not calculated if, for the linear case, the average case or control value is negative.		The fold change is not calculated if, for the linear case, the average case or control value is negative.
		+
		+
		+	At present, in geWorkbench-web, the fold-change data is only available via the Volcano Plot visualizer.

@@ Line 105: / Line 105: @@
 * Click '''Submit'''.
-==t-Test Results==
+=t-Test Results=
 A t-test result node is placed into the '''Workspace''' as a child of the analyzed microarray dataset.
 The list of significant markers is placed into a new set "Significant Genes" in  '''Marker Sets'''.  The number of markers in the set is shown in square brackets.
@@ Line 117: / Line 131: @@
 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 -log10(P-value).

← Older revision		Revision as of 20:04, 13 March 2015
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	==t-Test Results==		==t-Test Results==
−	~~==Result Sets==~~
	A t-test result node is placed into the '''Workspace''' as a child of the analyzed microarray dataset.		A t-test result node is placed into the '''Workspace''' as a child of the analyzed microarray dataset.