QuickStart - Revision history

Smith: /* Hints on using geWorkbench */

2014-05-16T21:39:44Z

‎Hints on using geWorkbench

Smith: /* Basic Principles */

2013-10-15T16:56:29Z

‎Basic Principles

Smith: /* Basic Principles */

2013-02-25T21:38:24Z

‎Basic Principles

Smith: /* Basic Principles */

2013-02-25T21:38:11Z

‎Basic Principles

Smith: /* Basic Principles */

2012-03-19T19:57:59Z

‎Basic Principles

Smith at 19:21, 13 March 2012

2012-03-13T19:21:39Z

Smith: /* Basic Principles */

2012-03-13T19:21:01Z

‎Basic Principles

Smith: /* Basic Principles */

2012-02-29T20:38:22Z

‎Basic Principles

Smith: /* Hints on using geWorkbench */

2010-06-17T20:58:39Z

‎Hints on using geWorkbench

Smith: /* Download and Installation */

2010-06-15T16:05:19Z

‎Download and Installation

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 # '''Microarray Annotation Files''': Most components that link to external data sources require that an annotation file be associated with the microarray file when it is loaded.  geWorkbench currently supports the Affymetrix annotation file format.  Examples of components that depend on annotation file information include Sequence Retriever, Marker Annotations, Cellular Network Knowledge Base, and Gene Ontology.  Instructions for obtaining Affymetrix annotation files are available in the [[FAQ#Q._Where_can_I_obtain_the_latest_annotation_files_for_my_microarray_platform.3F| geWorkbench FAQ]] section.
 # '''Visibility''': Only components relevant to the currently selected data node in the Project Folders component are displayed.  For instance, after a BLAST job, the active node is the BLAST node, and the BLAST viewer component will be shown.  Select the original, parent sequence data node again to see all its available components.
-# '''Support''': geWorkbench is actively support by the [https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page  caBIG Molecular Analysis Tools Knowledge Center].  We strongly encourage you to submit any questions or problems to the [https://cabig-kc.nci.nih.gov/Molecular/forums/  geWorkbench End User Discussion Forum].  You just need to sign up for a free account with the Knowledge Center to post a question.
+# '''Support''': geWorkbench is actively supported via the [https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page  caBIG Molecular Analysis Tools Knowledge Center].  We strongly encourage you to submit any questions or problems to the [https://cabig-kc.nci.nih.gov/Molecular/forums/  geWorkbench End User Discussion Forum].  You just need to sign up for a free account with the Knowledge Center to post a question.

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 The tutorials give a simple introduction to using geWorkbench.
-# '''With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.'''
+# Commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.
 # To choose which components of geWorkbench to load, see [[Component_Configuration_Manager| Component Configuration Manager]].
 # To load in a microarray data file, see [[Local_Data_Files| Local Data Files]].

@@ Line 9: / Line 9: @@
 The tutorials give a simple introduction to using geWorkbench.
-# '''With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.
+# '''With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.'''
 # To choose which components of geWorkbench to load, see [[Component_Configuration_Manager| Component Configuration Manager]].
 # To load in a microarray data file, see [[Local_Data_Files| Local Data Files]].

@@ Line 9: / Line 9: @@
 The tutorials give a simple introduction to using geWorkbench.
+# '''With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.
 # To choose which components of geWorkbench to load, see [[Component_Configuration_Manager| Component Configuration Manager]].
 # To load in a microarray data file, see [[Local_Data_Files| Local Data Files]].
@@ Line 16: / Line 17: @@
 # To manage sets of microarrays, for example to group them into case and control for a t-test, see [[Array Sets| Array Sets]].
 # To manage sets of markers, for example lists of significantly over-expressed genes, see [[Marker Sets | Marker Sets]].
 ==Hints on using geWorkbench==

@@ Line 16: / Line 16: @@
 # To manage sets of microarrays, for example to group them into case and control for a t-test, see [[Array Sets| Array Sets]].
 # To manage sets of markers, for example lists of significantly over-expressed genes, see [[Marker Sets | Marker Sets]].
-# With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.
+# With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.  Most analysis components have tutorial chapters explaining their use.
 ==Hints on using geWorkbench==

@@ Line 14: / Line 14: @@
 # To normalize your data, see [[Normalization | Normalization]].
 # To filter your data, see [[Filtering| Filtering]].
-# To manage sets of microarrays, for example to group them into case and control for a t-test, see [[Data_Subsets_-_Arrays| Data Subsets - Arrays]].
+# To manage sets of microarrays, for example to group them into case and control for a t-test, see [[Array Sets| Array Sets]].
-# To manage sets of markers, for example lists of signficantly over-expressed genes, see [[Data_Subsets_-_Markers | Data Subsets - Markers]].
+# To manage sets of markers, for example lists of signficantly over-expressed genes, see [[Marker Sets | Marker Sets]].
 # With release 2.3.0 of geWorkbench, commands for analysis, filtering and normalization of data are found in a right-click menu on any loaded data node.  The commands can also be accessed from the top menu-bar.

@@ Line 4: / Line 4: @@
 ==Download and Installation==
 Please see the [[Download_and_Installation|Download and Installation]] page for a full description of the requirements for running geWorkbench, and for a description of installation files.  Versions are available for Windows, Linux and Macintosh, and a Generic version can be run on any platform.
 ==Hints on using geWorkbench==