geWorkbench

Revision as of 16:19, 8 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

The SAM analysis component can use a local installation of R on your desktop computer.

This has been tested with R version 2.15.0 and 3.0.2.

There are special considerations for installing R on Windows computers, please see R installation on Windows.

Setting the R location in geWorkbench is covered at Preferences: R Location.

The full SAM Reults viewer is shown here.

The results can be sorted, e.g. on the fold change value as shown below.

@@ Line 23: / Line 23: @@
 ===SAM Results Viewer===
-The Full SAM Reults viewer is shown here.
+The full SAM Reults viewer is shown here.
 [[Image:SAM_Viewer_full.png]]