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	{{TutorialsTopNav}}		{{TutorialsTopNav}}
−	==Outline==	+	==Overview==
−	In this tutorial, you will learn how to:
−	*Create a new Project.
−	*Load microarray data.
−	*Merge data from several loaded microarray experiments.
−	*Rename a project and/or project node.
−	*Remove a project and/or project node.
−	*Save project files that you have created.
−	*Load, add, and/or modify remote data.
		+	The Workspace is located in the upper-left-hand corner of the application. It is used to contain open data files and store analysis results during a geWorkbench session. When geWorkbench is launched, an empty Workspace folder is displayed.
−	==Supported data formats==	+	[[Image:Workspace.png]]
−	*Microarray
−	**Affymetrix MAS5/GCOS Files.'''''This one will be used for the tutorial.'''''  ''brief explanation of file type needed''
−	**Affymetrix File Matrix - this is the native file type created by geWorkbench.
−	**RMA Express File - RMA Express is a sophisticated tool for combining data from multiple Affymetrix chips.
−	**Affy Excel or txt data file.
−	**Normalized no-confidence expression matrix. A variant of the geWorkbench file matrix format that omits the confidence value columns (P-value or Present/Absent calls).
−	**Genepix Files - An analysis program for two color arrays.
−	*Other
−	**FASTA Files. DNA or protein sequence files in FASTA format.
−	**Pattern Files.
−	**Genotypic data Files.
		+	The workspace as a whole, with all its projects and data nodes, can be saved and restored.  However, only one workspace can be open at one time.  Creating a new workspace or loading a saved workspace will overwrite the current workspace.
−	==Loading data files into a project==
−	In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset.
−	All data must belong to a project.  Right-click on the '''Workspace''' entry in the '''Project Folders''' window at upper left to create a new project.	+	* To view the next level down in the hierarchy, click on the “+” icon to expand the branch.
−	[[Image:T_NewProject.png]]	+	* To collapse a branch, click on the “-” icon.
		+	The Workspace may contain several heterologous datasets. These datasets can include input (source) data and derived data (results) associated with an experiment as well as image files. Source data can be loaded from the user’s local storage or from remote servers.  Loading datasets into the geWorkbench Workspace does not change their physical storage locations.
−	Next, right-click on the new project entry and select '''Open Files'''.	+	'''Note''' - The top menu-bar items [[Menu_Bar#File|File]] and [[Menu_Bar#Edit|Edit]] also apply to items in the Workspace.  They offer many of the same options shown below, except e.g. Microarray merging is only available from the top level [[Menu_Bar#File|File]] menu.
−	[[Image:T_OpenFiles.png]]	+	==Workspace Menu Options==
		+	Right-clicking on the Workspace node gives a menu with the following options
−	Here, we will select file type '''Affy GCOS/MAS5''' as shown.
−	Make sure to check the '''Merge files''' checkbox.	+	[[Image:Workspace_right_click_menu.png]]
−	We select 10 MAS5 format text files from the directory geworkbench\data\training\cardiogenomics.med.harvard.edu, which is included in the geWorkbench download.
−	Click '''Open'''.	+	===Open Files===
		+	* Loading data from local files is covered in the chapter [[Local_Data_Files | Local Data Files]]
		+	* Retrieving data from remote sources (caArray) is covered in [[Remote_Data_Sources | Remote Data Sources]]
−	[[Image:T_SelectMAS5.png]]
		+	===Open PDB File from RCSB Protein Data Bank===
		+	If '''Open PDB File from RCSB Protein Data Bank''' is chosen, a dialog box appears.
−	The chip type HG_U95Av2 is recognized...	+	[[Image:Project_Folders_Project_Open_RCSB_PDB.png]]
−	[[Image:T_Chip_type_message.png]]
		+	Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.
		+	==Workspace Data Node Menu Options==
−	The merged dataset is listed in the Project folder. The data is displayed, in single array format, in the '''Microarray Viewer'''.  Note we have increased the intensity slider to maximum here.	+	Right-clicking on a data node will produce a popup menu with the following options:
−	[[Image:T_MAS5_display.png]]
		+	[[Image:Workspace_data_node_right_click.png]]
−	==Merging microarray datafiles after they have been loaded.==	+	===Save===
−	If Affymetrix data files are not merged at the time they are read in, they can also be merged later, as long as they are from the same chip type.	+	Save the currently selected data node.  This is implemented for at least the below data types.  If saving of a particular type has not been implemented, the "Save" option will be disabled (grayed-out).
−	'''''<u>To merge data from individual experiments already loaded</u>'''''	+	* '''Microarray gene expression''' -  data is saved using the geWorkbench ".exp" format, regardless of the original format. This allows saving e.g. a merged dataset, and/or any array and marker sets that may have been created.
		+	* '''FASTA''' - saved in FASTA format (.fasta).
		+	* '''PDB''' - saved in PDB format (.pdb).
		+	* '''Network''' - saved using the Adjacency Matrix "ADJ" format (.adj).
		+	* '''t-test result''' - saved as comma separated value (.csv) file.
		+	* '''Image''' - saved as PNG file (.png).
−	'''1.''' Select the read-in data files that you want to merge.	+	For each file type, a file browser with a filter for the target file type extension (e.g. .fasta) will be opened.
−	'''2.''' Click on '''File''' in the menu bar, and choose '''Merge Datasets'''.	+	===Export to tab-delim===
		+	This option will only appear for microarray gene expression datasets. It allows the microarray dataset to be exported in a spreadsheet format, as a tab-delimited text file.  The first row contains array names and the first column contains the marker names.
−	The picture shows the resulting merged dataset created from several individual data files.	+	This export format does not preserve array or marker sets that may have been defined in geWorkbench for the dataset.  However, it can be used to save a copy of e.g. merged, filtered, and/or normalized data in a format easily used by other programs.
−	[[Image:(T)MFileScreen1.png]]	+	When exporting, the file save dialog will display the name of the dataset, minus any recognized file-type suffixes that may be present (e.g. .soft).
		+	===Rename===
−	==Renaming a project or a data node==	+	A dialog box will appear in which a new name can be entered.
−	===Renaming a Project===	+	[[Image:Workspace_Rename_Node.png]]
−	'''1.''' Right-click on '''Project''' folder.	+	===Remove===
−	'''2.''' Select '''Rename'''.	+	The selected data nodes and any child data nodes will be removed. Multiple selections can be made.
		+	==Data Node Hover-text Information==
−	[[Image:(T)MReNameProject.png]]	+	For microarray datasets, adjacency matrices (network nodes), sequence and pattern nodes, moving the mouse cursor over the data nodes will display additional details about a dataset.
		+	Microarray datasets: hover text displays number of markers and arrays.
−	'''3.''' In the pop-up screen rename your project.
−	'''4.''' Click on the '''Okay''' button	+	[[Image:Dataset_hover_microarray.png]]
		+	Adjacency Matrix: hover text displays number of nodes and edges in the network.
−	===Renaming a project data node===
−	'''1.''' Right-click on '''Project''' node.	+	[[Image:Workspace_Dataset_hover_network.png]]
−	'''2.''' Select '''Rename'''.
		+	Sequence node:
−	[[Image:(T)MReNameProjectNode.png]]
		+	[[Image:Workspace_hover_sequences.png]]
−	'''3.''' In the pop-up screen rename your project node.
−	'''4.''' Click on the '''Okay''' button.	+	Pattern node:
−	==Removing a project or a data node==
		+	[[Image:Workspace_Pattern_Hover.png]]
−	===Removing a project===	+	==Workspaces==
−	'''1.''' Right-click on '''Project''' folder.	+	===Saving the Workspace===
−	'''2.''' Select '''Remove'''.	+	Saving the workspace saves all its data to a file on disk. The workspace can later be reloaded to resume work.
−	'''3.''' You will no longer see the project folder.	+	====Special considerations on saving and restoring workspaces====
		+	* '''Versions''' - Workspaces in general may not be compatible across different versions of geWorkbench.
		+	* '''Loaded components''' - The configuration in the [[Component_Configuration_Manager| CCM]] of which components are loaded and which are not is not saved when the workspace is saved; it is maintained separately.
		+	* '''Changes to loaded components''' - If a workspace is saved, and then changes are made to which components are loaded in the [[Component_Configuration_Manager| CCM]], then in rare cases problems may occur when one attempts to reload the saved workspace.
		+	[[Image:File_Save_Workspace.png]]
−	===Removing a project data node===	+	===Opening a Saved Workspace===
−	'''1.''' Right mouse click on the data node.	+	File->Open-Workspace.
−	'''2.''' Select '''Remove'''.	+	Only one workspace at a time can be loaded in geWorkbench. Opening a saved workspace will destroy the existing workspace.  For this reason, if you opt to open a workspace, you will be prompted as to whether to save the existing workspace first.
−	'''3.''' You will no longer see the data node.
		+	[[Image:File_Open_Workspace.png]]
		+	A dialog box will appear in which the location and file name to which to save the workspace can be chosen.
−	==Saving a data node to a file==
−	'''1.''' Right-click on data nodes that you want to save.	+	[[Image:File_Save_Workspace_Dialog.png]]
−	'''2.''' Click '''Save'''.	+	===Creating a New Workspace===
		+	Only one workspace at a time can be loaded in geWorkbench.  Creating a new workspace will destroy the existing workspace.  For this reason, if you opt to create a new workspace, you will be prompted as to whether to save the existing workspace first.
		+	A new workspace can only be created from the top level menu bar.
−	[[Image:(T)MSavingAFile.png]]
		+	[[Image:File_New_Workspace.png]]
−	The '''Save''' screen will come up.
−		+	Select '''File->New->Workspace'''.
−	[[Image:(T)MSavingAFile1.png]]
−
−
−	'''3.''' Choose a location.
−
−	'''4.''' Enter a name.
−
−	'''5.''' Click on the '''Save''' button.
−
−
−
−	==Load, add, and/or modify remote data==
−
−
−	geWorkbench can retrieve data from certain remote data sources, for example instances of the NCI's caArray database.
−
−	As before, right-click on '''Project''' which will bring up the '''Open File''' dialog.  Click the '''Remote''' radio button.  The Open File dialog window will be expanded to include remote sources.
−
−	[[Image:(T)MEditRemoteData.png]]
−
−	Four additional buttons appear.  They are:
−
−	'''caArray''' button - Gives you a listing of your Remote Resources.
−
−	'''Go''' button - Accesses the Remote Source that you selected.
−
−	'''Add A New Resource''' button - Opens the Data Source Definition Page used to add Remote Data.
−
−	'''Edit''' button - Edits Remote Source Parameters.
−
−
−	===To Add A Remote Source===
−
−	'''1.''' Click on the '''Add A New Resource''' button.
−
−	[[Image:(T)MRemoteData2.png]]
−	This is the Data Source Definition Page
−
−	'''2.''' Fill in the Data Source definition page. URL and Short Name are required fields.
−
−	'''3.''' Click on the OK button.
−
−	The configuration is set up to automatically reflect your additional Data Source.
−
−
−
−	===To Modify A Remote Source===
−
−	The specification of the remote resource can be edited.
−
−	[[Image:(T)MRemoteData1.1.png]]
−
−	'''1.''' Click on the '''Edit''' button.
−
−
−	[[Image:(T)MRemoteData3.png]]
−
−	'''2.''' Make the changes that you need.
−
−	'''3.''' Click on the '''OK''' button

---

Latest revision as of 17:07, 10 January 2014

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot

Overview

The Workspace is located in the upper-left-hand corner of the application. It is used to contain open data files and store analysis results during a geWorkbench session. When geWorkbench is launched, an empty Workspace folder is displayed.

The workspace as a whole, with all its projects and data nodes, can be saved and restored. However, only one workspace can be open at one time. Creating a new workspace or loading a saved workspace will overwrite the current workspace.

• To view the next level down in the hierarchy, click on the “+” icon to expand the branch.

• To collapse a branch, click on the “-” icon.

The Workspace may contain several heterologous datasets. These datasets can include input (source) data and derived data (results) associated with an experiment as well as image files. Source data can be loaded from the user’s local storage or from remote servers. Loading datasets into the geWorkbench Workspace does not change their physical storage locations.

Note - The top menu-bar items File and Edit also apply to items in the Workspace. They offer many of the same options shown below, except e.g. Microarray merging is only available from the top level File menu.

Workspace Menu Options

Right-clicking on the Workspace node gives a menu with the following options

Open Files

• Loading data from local files is covered in the chapter Local Data Files
• Retrieving data from remote sources (caArray) is covered in Remote Data Sources

Open PDB File from RCSB Protein Data Bank

If Open PDB File from RCSB Protein Data Bank is chosen, a dialog box appears.

Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.

Workspace Data Node Menu Options

Right-clicking on a data node will produce a popup menu with the following options:

Save

Save the currently selected data node. This is implemented for at least the below data types. If saving of a particular type has not been implemented, the "Save" option will be disabled (grayed-out).

• Microarray gene expression - data is saved using the geWorkbench ".exp" format, regardless of the original format. This allows saving e.g. a merged dataset, and/or any array and marker sets that may have been created.
• FASTA - saved in FASTA format (.fasta).
• PDB - saved in PDB format (.pdb).
• Network - saved using the Adjacency Matrix "ADJ" format (.adj).
• t-test result - saved as comma separated value (.csv) file.
• Image - saved as PNG file (.png).

For each file type, a file browser with a filter for the target file type extension (e.g. .fasta) will be opened.

Export to tab-delim

This option will only appear for microarray gene expression datasets. It allows the microarray dataset to be exported in a spreadsheet format, as a tab-delimited text file. The first row contains array names and the first column contains the marker names.

This export format does not preserve array or marker sets that may have been defined in geWorkbench for the dataset. However, it can be used to save a copy of e.g. merged, filtered, and/or normalized data in a format easily used by other programs.

When exporting, the file save dialog will display the name of the dataset, minus any recognized file-type suffixes that may be present (e.g. .soft).

Rename

A dialog box will appear in which a new name can be entered.

Remove

The selected data nodes and any child data nodes will be removed. Multiple selections can be made.

Data Node Hover-text Information

For microarray datasets, adjacency matrices (network nodes), sequence and pattern nodes, moving the mouse cursor over the data nodes will display additional details about a dataset.

Microarray datasets: hover text displays number of markers and arrays.

Adjacency Matrix: hover text displays number of nodes and edges in the network.

Sequence node:

Pattern node:

Workspaces

Saving the Workspace

Saving the workspace saves all its data to a file on disk. The workspace can later be reloaded to resume work.

Special considerations on saving and restoring workspaces

• Versions - Workspaces in general may not be compatible across different versions of geWorkbench.
• Loaded components - The configuration in the CCM of which components are loaded and which are not is not saved when the workspace is saved; it is maintained separately.
• Changes to loaded components - If a workspace is saved, and then changes are made to which components are loaded in the CCM, then in rare cases problems may occur when one attempts to reload the saved workspace.

Opening a Saved Workspace

File->Open-Workspace.

Only one workspace at a time can be loaded in geWorkbench. Opening a saved workspace will destroy the existing workspace. For this reason, if you opt to open a workspace, you will be prompted as to whether to save the existing workspace first.

A dialog box will appear in which the location and file name to which to save the workspace can be chosen.

Creating a New Workspace

Only one workspace at a time can be loaded in geWorkbench. Creating a new workspace will destroy the existing workspace. For this reason, if you opt to create a new workspace, you will be prompted as to whether to save the existing workspace first.

A new workspace can only be created from the top level menu bar.

Select File->New->Workspace.