CaArray - Revision history

Smith at 20:04, 22 April 2014

2014-04-22T20:04:04Z

2014-04-17T23:18:43Z

‎Downloading select array datasets

2014-04-17T23:12:26Z

‎Downloading select array datasets

2013-10-16T21:12:32Z

2013-10-16T20:58:33Z

‎Connecting with caArray

2012-07-09T18:54:22Z

‎Searching and viewing available experiments

2012-07-09T18:51:34Z

‎Searching and viewing available experiments

2012-07-09T18:51:19Z

‎Searching and viewing available experiments

2012-07-09T18:48:32Z

‎Setting up the connection

2012-07-09T18:43:46Z

‎Downloading select array datasets

@@ Line 19: / Line 19: @@
 ==Connecting with caArray==
-The "Open File" dialog can be reached by selecting the Workspace node and then either right-clicking, or using "File->Open File(s)" in the top menu bar.
+The "Open File" dialog can be reached by selecting the [[Workspace]] node and then either right-clicking, or using "File->Open File(s)" in the top menu bar.
@@ Line 146: / Line 146: @@
-The resulting data set will appear in the Workspace.
+The resulting data set will appear in the [[Workspace]].
 The downloaded dataset is name for the experiment name shown in caArray.

@@ Line 126: / Line 126: @@
-As of geWorkbench 2.4.0, you will also be prompted to specify the type of annotation file type.  The two supported annotation file types are
+As of geWorkbench 2.4.0, you will also be prompted to specify the type of annotation file type.
 * Affymetrix 3' Expression
-* Affymetrix WT Gene/Exon ST, transcript level
+The two supported annotation file types are
 Here we select the 3' Expression format.

@@ Line 128: / Line 128: @@
 As of geWorkbench 2.4.0, you will also be prompted to specify the type of annotation file type.  The two supported annotation file types are
 * Affymetrix 3' Expression
-* Affymetrix Gene/Exon 1.0 ST
+* Affymetrix WT Gene/Exon ST, transcript level
 Here we select the 3' Expression format.

@@ Line 19: / Line 19: @@
 ==Connecting with caArray==
-To connect to a remote caArray, right-click on '''Project''' in the geWorkbench main window,
+The "Open File" dialog can be reached by selecting the Workspace node and then either right-clicking, or using "File->Open File(s)" in the top menu bar.
 [[Image:Workspace_Open_Files.png]]
-which will bring up the '''Open File(s)''' dialog.   Click the '''caArray 2.5''' radio button.   The '''Open File''' dialog window will be expanded to include remote caArray sources as shown here.
+Click the '''caArray 2.5''' radio button.   The '''Open File''' dialog window will be expanded to include remote caArray sources as shown here.
@@ Line 143: / Line 143: @@
-The resulting data set will appear in the Project Folders component.
+The resulting data set will appear in the Workspace.
 The downloaded dataset is name for the experiment name shown in caArray.

@@ Line 22: / Line 22: @@
-[[Image:T_ProjectFolders_OpenFiles.png]]
+[[Image:Workspace_Open_Files.png]]
 which will bring up the '''Open File(s)''' dialog.   Click the '''caArray 2.5''' radio button.   The '''Open File''' dialog window will be expanded to include remote caArray sources as shown here.
@@ Line 29: / Line 28: @@
 [[Image:Open_File_caArray.png]]
 ==Connection and Query Controls==

@@ Line 83: / Line 83: @@
 ==Searching and viewing available experiments==
-If you click on the red '''Go''' button next to the caArray data source at the bottom of the dialog, all available caArray experiments at that location will be displayed.
+If you click on the '''Go''' button next to the caArray data source at the bottom of the dialog, all available caArray experiments at that location will be displayed.
 Instead, you can select only particular kinds of experiments by pushing the '''Filter''' button.  Here we show experiments of type "Human" being selected.
@@ Line 91: / Line 91: @@
-And here are the resulting entries in the database.  Note that the '''caArray Experiment ID''' of the selected experiment is shown in the upper right-hand corner of the dialog.
+The below figure shows the matching entries in the database.

← Older revision		Revision as of 18:51, 9 July 2012
Line 91:		Line 91:


−	And here are the resulting entries in the database. Note that the caArray Experiment ID of the selected experiment is shown in the upper right-hand corner of the dialog.	+	And here are the resulting entries in the database. Note that the '''caArray Experiment ID''' of the selected experiment is shown in the upper right-hand corner of the dialog.

@@ Line 79: / Line 79: @@
 * '''Port''' - the port on the remote caArray server at which caArray is available.
 * '''Username''' and '''Password''' (optional) - caArray supports retrieval of data from private experiments.  These fields allow the user to provide his or her caArray credentials to gain access to any private experiments to which he or she has rights.  No username or password is needed for accessing public experiments.
-** '''Note''' -  Once a username and password have been entered and submitted to caArray, you cannot go back to using no username/password, except by restarting geWorkbench.  However you can still put in a different username/password combination.  This is a property of the caArray server-side code.  Thus if you have no valid username/password and enter an incorrect one, you will need to restart geWorkbench before you can query caArray public experiments again (no login required).
+** '''Note''' -  Once a username and password have been entered and submitted to caArray, you cannot go back to using no username/password, except by restarting geWorkbench.  However you can still put in a different username/password combination.  This is a property of the caArray server-side code.
 ==Searching and viewing available experiments==

← Older revision		Revision as of 18:43, 9 July 2012
Line 149:		Line 149:


−	[[Image:~~Open_File_Remote_caArray_merged_node~~.png]]	+	[[Image:Open_File_caArray_merged_node.png]]

	==Cannot merge different array types==		==Cannot merge different array types==