MatrixREDUCE - Revision history

Smith: /* Parameters */

2014-05-12T17:26:56Z

‎Parameters

Smith at 23:51, 22 January 2014

2014-01-22T23:51:53Z

Ut2102: /* Example */

2013-07-16T19:35:04Z

‎Example

Smith: /* Example */

2012-03-01T23:47:19Z

‎Example

Smith: moved Tutorial - MatrixREDUCE to MatrixREDUCE

2010-12-09T22:06:21Z

moved Tutorial - MatrixREDUCE to MatrixREDUCE

Smith: /* Parameters */

2009-07-30T21:56:55Z

‎Parameters

Smith: /* Example */

2009-07-17T19:30:00Z

‎Example

Smith: /* Example */

2009-07-17T19:29:46Z

‎Example

Smith: /* Example */

2009-07-17T19:29:03Z

‎Example

Smith: /* Example */

2009-07-17T19:26:29Z

‎Example

← Older revision		Revision as of 17:26, 12 May 2014
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	'''Save run log''' - diagnostic messages from the run will be saved to a file.		'''Save run log''' - diagnostic messages from the run will be saved to a file.

		+
		+	==Note on Activating Marker Sets==
		+	The local version of MatrixREDUCE ignores activated marker sets entirely. In the "grid" version, activating a marker set affects the result shown in the PSAM Detail tab, but not in the sequence tab.
		+
		+	The user is advised not to activate marker sets during MatrixREDUCE runs.

	==Services (Grid)==		==Services (Grid)==

@@ Line 84: / Line 84: @@
 ====Image Snapshot====
-'''Take Snapshot''' - Places an image of the sequence view in the Project folders component.
+'''Take Snapshot''' - Places an image of the sequence view in the [[Workspace]].
 ==Example==
@@ Line 91: / Line 91: @@
-. In the Project Folders component, either use an existing Project, or create a new one.
+. Right-click on the [[Workspace]] node and select "Open File(s)".
-. Right-click on Project and select "Open File(s)".
+. Browse to where you saved the file SpellmanReduced.txt and set the file type to "Tab-Delimted".    Open the file.
-. Browse to where you saved the file SpellmanReduced.txt and set the file type to "Tab-Delimted".    Open the file.
+. You will be asked for an annotations file.  This is not needed for this example, so you can hit Cancel.
-. You will be asked for an annotations file.  This is not needed for this example, so you can hit Cancel.
+. Go to the Analysis tab and select Matrix Reduce.
-. Go to the Analysis tab and select Matrix Reduce.
+. To load the sequence file, click the "Load..." button.  Browse to the sequence file "Y5_600_Bst.txt" and open it.
@@ Line 108: / Line 106: @@
 . Click Analyze to run MatrixREDUCE. (If you are running geWorkbench from a console window using ANT, you can follow the progress of the calculations there).
-. The result is placed as a node beneath the parent microarray dataset in the Project Folders component.  At the same time, the results are displayed in the Visual Area of geWorkbench.
+. The result is placed as a node beneath the parent microarray dataset in the [[Workspace]].  At the same time, the results are displayed in the Visual Area of geWorkbench.
 There are two tabs in the viewer, '''PSAM Detail''' and '''Sequence'''.  Within PSAM Detail there are two options.  The first is the Image view, which depicts the PSAM graphically.

← Older revision		Revision as of 19:35, 16 July 2013
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−	[[Image:MatrixREDUCE_Parameters.png]]	+	[[Image:MatrixREDUCE_Parameters.png\|{{ImageMaxWidth}}]]

← Older revision		Revision as of 23:47, 1 March 2012
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−	[[Image:~~T_MatrixREDUCE_Parameters~~.png]]	+	[[Image:MatrixREDUCE_Parameters.png]]

← Older revision		Revision as of 21:56, 30 July 2009
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	'''Save run log''' - diagnostic messages from the run will be saved to a file.		'''Save run log''' - diagnostic messages from the run will be saved to a file.
		+
		+
		+	==Services (Grid)==
		+
		+	MatrixREDUCE can be run either locally within geWorkbench, or remotely as a grid job on caGrid. See the [[Tutorial_-_Grid_Services \| Grid Services]] section for further details on setting up a grid job.

	==Graphical Interface for results==		==Graphical Interface for results==

← Older revision	Revision as of 22:06, 9 December 2010
(No difference)

← Older revision		Revision as of 19:30, 17 July 2009
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	==Example==		==Example==

−	In this example, we will use two files that are available here. Right-click on each link and select "Save ~~file~~ as". Download them into a convenient directory. They are [[Media:SpellmanReduced.txt \| SpellmanReduced.txt]] and [[Media:Y5_600_Bst.txt \| Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.	+	In this example, we will use two files that are available here. Right-click on each link and select "Save link as". Download them into a convenient directory. They are [[Media:SpellmanReduced.txt \| SpellmanReduced.txt]] and [[Media:Y5_600_Bst.txt \| Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.

← Older revision		Revision as of 19:29, 17 July 2009
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	==Example==		==Example==

−	In this example, we will use two files that are available here. Right-click on each link and select "Save file as". Download them into a convenient directory. They are [[Media:SpellmanReduced.txt \| SpellmanReduced.txt]] and [[~~Meida~~:Y5_600_Bst.txt \| Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.	+	In this example, we will use two files that are available here. Right-click on each link and select "Save file as". Download them into a convenient directory. They are [[Media:SpellmanReduced.txt \| SpellmanReduced.txt]] and [[Media:Y5_600_Bst.txt \| Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.

← Older revision		Revision as of 19:26, 17 July 2009
Line 83:		Line 83:
	==Example==		==Example==

−	In this example, we will use two files that are available here. Right-click on each link and select "Save file as". Download them into a convenient directory. They are [[~~Media~~:SpellmanReduced.txt]] and [[~~Media~~:Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.	+	In this example, we will use two files that are available here. Right-click on each link and select "Save file as". Download them into a convenient directory. They are [[Image:SpellmanReduced.txt \| SpellmanReduced.txt]] and [[Image:Y5_600_Bst.txt \| Y5_600_Bst.txt]]. SpellmanReduced.txt contains a subset of the data from Spellman 1998. Y5_600_Bst.txt contains the corresponding upstream DNA sequences for these genes.