QuickStart

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



Download and Installation

Please see the 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.


Basic Principles

The tutorials give a simple introduction to using geWorkbench.

  1. 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.
  2. To choose which components of geWorkbench to load, see Component Configuration Manager.
  3. To load in a microarray data file, see Local Data Files.
  4. To normalize your data, see Normalization.
  5. To filter your data, see Filtering.
  6. To manage sets of microarrays, for example to group them into case and control for a t-test, see Array Sets.
  7. To manage sets of markers, for example lists of significantly over-expressed genes, see Marker Sets.

Hints on using geWorkbench

  1. Components: Not all geWorkbench components are loaded by default. Additional available components can be loaded by using the Component Configuration Manager (CCM).
  2. 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 geWorkbench FAQ section.
  3. 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.
  4. Support: geWorkbench is actively supported via the caBIG Molecular Analysis Tools Knowledge Center. We strongly encourage you to submit any questions or problems to the 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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