Revision as of 16:29, 13 August 2008

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

Outline

In this tutorial, you will learn how to:

Create a new Project.
Rename a project and/or project node.
Remove a project and/or project node.
Save project files that you have created.

Overview

This section covers three areas - (1) the logical organization of data within geWorkbench into projects and workspaces, (2)working with data files in this logical structure, and (3) special handling of microarray data files, including obtaining data from local and remote sources, and merging multiple data files into one. These topics are bundled into one because these various operations are all handled within the same Project Folders component.

Workspaces and Projects

In the Project Folders component there is a top-level object called a workspace. The workspace can contain one or more separate projects, and each project can contain opened data files and analysis results. An analogy might be that a workspace is like a drawer in a filing cabinet, and projects are individual folders in that drawer. Projects allow data to be grouped, for example by experiment. A project can contain many different types of data, for example microarray data, FASTA sequence files and graphical images. 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.

Microrray data and merging

When working with microarray data, all data to be analyzed must be present within one data node in a project. If the data exists as multiple files containing results 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.

Supported data formats

Microarray
- Affymetrix MAS5/GCOS files - produced by the Affymetrix data analysis programs.
- Affymetrix File Matrix - a spreadsheet-type multi-experiment format; this is the native file type created by geWorkbench from merged datasets.
- Tab-delimited text (RMAExpress file) - A simple columnar file format, as produced by the program RMAExpress.
- Genepix .GPR files - Produced by a popular analysis program for two-color microarrays.
- Affymetrix CEL files - these files of probe level data can be viewed graphically in geWorkbench but not used directly for analysis.
Other
- FASTA files. DNA or amino-acid sequence files in FASTA format.
- PDB files - protein 3-dimensional structure files can be viewed in the JMol Viewer in geWorkbench.
- NetBoost Edge List - used by a component still under development.

Tutorial: Working with Projects

Creating a new project

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.

Renaming a project

1. Right-click on Project folder.

2. Select Rename.

3. In the pop-up screen rename your project.

4. Click on the OK button

Renaming a project data node

1. Right-click on a Project Folder data node.

2. Select Rename.

3. In the pop-up screen rename your data node.

4. Click on the OK button.

Removing a project

1. Right-click on Project folder.

2. Select Remove.

Removing a project data node

1. Right-click on the data node.

2. Select Remove.

Saving a data node to a file

It is here that, among other things, you can create the matrix multi-experiment file format used by geWorkbench from a merged dataset.

1. Right-click on data node that you want to save.

2. Click Save.

A standard file Save screen will come up.

3. Choose a location.

4. Enter a name.

5. Click on the Save button.

@@ Line 5: / Line 5: @@
 *Create a new Project.
-*Load microarray data.
-*Merge data from several loaded microarray experiments.
-*Download data from a remote instance of the caArray database (supported by NCI).
 *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.
@@ Line 114: / Line 111: @@
 '''5.''' Click on the '''Save''' button.
-=Tutorial: Loading microarray data files - local=
-In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset.  The origin of these file is described in the section [[Tutorial_-_Data]]
-Next, right-click on the '''New Project''' entry and select '''Open Files'''.
-[[Image:T_OpenFiles.png]]
-A file browser will appear with which you can select the files you wish to open.  The default is to browse for local files, that is on your own computer.  geWorkbench can also access data from caArray databases.
-[[Image:T_OpenFile_MAS5.png]]
-Here, we will select file type '''Affymetrix GCOS/MAS5''' as shown.
-Make sure to check the '''Merge files''' checkbox.  This will create the merged data node as the files are read in.
-We will select 10 MAS5 format text files from the directory cardiogenomics.med.harvard.edu, which is included in the geWorkbench tutorial download.
-Click '''Open'''.
-A message will appear giving information about associating an annotation file with the dataset.
-[[Image:T_Annotation-selection1.png]]
-A file browser will then open with which you can, if you wish, select an annotation file matching your dataset.  This is needed if you intend to use features of geWorkbench such as the Sequence Retriever or  GO Terms component (Gene Ontology).
-[[Image:T_Annotation-selection2.png]]
-A status bar will display as the data is loaded:
-[[Image:T_File-loading-status-bar.png]]
-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.  You can scroll through the arrays from first to last using the slider.  The display in the '''Microarray Viewer''' is by marker in the linear order the markers appear in the data file.  It does not correspond in any way to a physical picture or representation of the actual 2-D microarray.
-[[Image:T_Merged_MAS5_files.png]]
-=Tutorial: Merging microarray data files after they have already been loaded.=
-If 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.
-'''1.''' Select the read-in data files that you want to merge.
-'''2.''' Click on '''File''' in the menu bar, and choose '''Merge Datasets'''.
-The picture shows the resulting merged dataset created from several individual data files.
-[[Image:T_MergeIndividual.png]]
-The result is a new data node containing the merged data.  The original data nodes are still present.
-[[Image:T_ProjectFolder_IndividMerged.png]]

geWorkbench

Difference between revisions of "Workspace"