Local Data Files - Revision history

Smith: /* Microarray Data Annotation Files */

2015-01-28T00:45:24Z

‎Microarray Data Annotation Files

Smith: /* Microarray Data Annotation Files */

2015-01-28T00:44:29Z

‎Microarray Data Annotation Files

Smith at 20:01, 22 April 2014

2014-04-22T20:01:23Z

Smith: /* Microarray Data Annotation Files */

2014-04-17T23:16:02Z

‎Microarray Data Annotation Files

Smith: /* Microarray Data Annotation Files */

2014-04-17T23:15:19Z

‎Microarray Data Annotation Files

Smith: /* Microarray Data Annotation Files */

2014-04-17T23:14:28Z

‎Microarray Data Annotation Files

Smith: /* Pattern Files */

2013-10-16T20:47:03Z

‎Pattern Files

Smith: /* Example */

2013-10-16T20:46:17Z

‎Example

Smith: /* Merging Microarray Files */

2013-10-16T20:45:43Z

‎Merging Microarray Files

Smith: /* Overview */

2013-10-16T20:45:08Z

‎Overview

← Older revision		Revision as of 00:45, 28 January 2015
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−	Next ~~(as of geWorkbench 2.4.0)~~, you will ~~also~~ be prompted to specify the type of annotation file type.	+	Next, you will be prompted to specify the type of annotation file type.

	Here we select the 3' Expression format.		Here we select the 3' Expression format.

← Older revision		Revision as of 00:44, 28 January 2015
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−	[[Image:~~File_Open_Annotation_File_Browser~~.png]]	+	[[Image:File_Open_Annotation.png]]

@@ Line 11: / Line 11: @@
 The Open File dialog can be reached in two ways:
-* Right-click on the Workspace node and select "Open File(s)".
+* Right-click on the [[Workspace]] node and select "Open File(s)".
 [[Image:Workspace_Open_Files.png]]
@@ Line 247: / Line 247: @@
 A network file must be loaded as the child of a microarray dataset.  This allows a mapping of network nodes to microarray dataset markers (probesets).  A marker set defined in the Markers component can be projected onto a network displayed in Cytoscape, and a selection of nodes in Cytoscape is returned automatically to the Markers component.  Many other operations are available.
-Adjacency matrices are loaded by first selecting the Workspace node, and then using either the menu-bar or right-click File->Open dialog.   A microarray dataset chooser allows the user to select to which dataset to add the network.
+Adjacency matrices are loaded by first selecting the [[Workspace]] node, and then using either the menu-bar or right-click File->Open dialog.   A microarray dataset chooser allows the user to select to which dataset to add the network.
 ===Representation of networks in geWorbench===
@@ Line 270: / Line 270: @@
-* Select the Workspace node and then right-click.  Select "Open Files".  The Open File dialog will appear.
+* Select the [[Workspace]] node and then right-click.  Select "Open Files".  The Open File dialog will appear.
@@ Line 295: / Line 295: @@
 The figure above shows one of two available microarray datasets being chosen.  Here we use the Bcell-100 dataset.
-The network is shown below loaded as a child of the chosen dataset in the Workspace.
+The network is shown below loaded as a child of the chosen dataset in the [[Workspace]].
@@ Line 306: / Line 306: @@
 In the Pattern Discovery component, individual or multiple patterns can be saved to a text file.  This file also contains the name of the sequence file from which they were generated (parent data set).
-Before loading a pattern file, the matching sequence file must already be present in the Workspace.
+Before loading a pattern file, the matching sequence file must already be present in the [[Workspace]].
 In the "File Open" dialog, Pattern Files (*.pat) can be opened and reassociated with their parent sequence file.  As with loading network files, when loading a pattern file, the user will be prompted to select a parent data node.
@@ Line 360: / Line 360: @@
 Note that no Affymetrix annotation files are included in the geWorkbench distribution.  The annotation file for the HG-U95Av2 array used in this example can be obtained from the Affymetrix website.  See the instructions in the [[FAQ#Q._Where_can_I_obtain_the_latest_annotation_files_for_my_microarray_platform.3F | FAQ entry on this topic]].
-. Right-click on the Workspace node and select '''Open Files'''.
+. Right-click on the [[Workspace]] node and select '''Open Files'''.
 [[Image:Workspace_Open_Files.png]]
@@ Line 404: / Line 404: @@
-. The merged data set is listed in the Workspace. The individual arrays are shown below in the Arrays component.
+. The merged data set is listed in the [[Workspace]]. The individual arrays are shown below in the Arrays component.

@@ Line 101: / Line 101: @@
 geWorkbench currently can utilize two types of Affymetrix annotation file:
-* Affymetrix 3' Expression (CSV format)
+* '''Affymetrix 3' Expression''' (CSV format)
-* Affymetrix WT Gene/Exon ST, transcript level, CSV-format) - This parser supports both the Gene 1.0 ST and Gene 2.0 ST annotation files (same format).
+* '''Affymetrix WT Gene/Exon ST, transcript level''' (CSV-format) - This parser supports both the Gene 1.0 ST and Gene 2.0 ST annotation files (same format).
 Other platform types and manufacturers are not supported.  See [[File_Formats#Annotation_Files | File Formats]] for further details on the actual file formats accepted.  For some purposes, you can create files in the Affymetrix 3' Expression format for other platform types.

← Older revision		Revision as of 23:15, 17 April 2014
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	[[Image:Open_File_Select_Annotation_Type.png]]		[[Image:Open_File_Select_Annotation_Type.png]]
−
−
−	~~As noted above, the Gene/Exon 1.0 ST parser also supports the Affymetrix Gene 2.0 ST transcript-level CSV-format annotation files.~~

← Older revision		Revision as of 20:46, 16 October 2013
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	The figure above shows one of two available microarray datasets being chosen. Here we use the Bcell-100 dataset.		The figure above shows one of two available microarray datasets being chosen. Here we use the Bcell-100 dataset.

−	The network is shown below loaded as a child of the chosen dataset in the ~~Project Folders component~~.	+	The network is shown below loaded as a child of the chosen dataset in the Workspace.

@@ Line 55: / Line 55: @@
 If multiple microarray gene expression files are read in at the same time, they will be merged into a single dataset. This can be done by multiple selecting the desired files in the file open dialog.
-Background - When working with microarray data in geWorkbench, all data to be analyzed must be present within one data node in a project.  If the data exists as multiple files each containing results e.g. from single arrays, the data must be merged into a single node before it can be used.  geWorkbench can perform this merging step either at the time data is read in, or later in a separate step.  Once merged, such a dataset can be saved to disk; it will be saved in the geWorkbench matrix file format.
+Background - When working with microarray data in geWorkbench, all data to be analyzed must be present within one data node.  If the data exists as multiple files each containing results e.g. from single arrays, the data must be merged into a single node before it can be used.  geWorkbench can perform this merging step either at the time data is read in, or later in a separate step.  Once merged, such a dataset can be saved to disk; it will be saved in the geWorkbench matrix file format.
 Requirements for merging microarray data files are: