geWorkbench

Revision as of 17:48, 22 October 2013

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 15: / Line 15: @@
 Setting the R location in geWorkbench is covered at [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29| Preferences: R Location]].
+===SAM Parameters===
+[[Image:SAM_Analysis_Parameters.png]]
+===SAM Results Viewer===
+The Full SAM Reults viewer is shown here.
+[[Image:SAM_Viewer_full.png]]
+The results can be sorted, e.g. on the fold change value as shown below.
+[[Image:SAM_Viewer_Overexpressedl.png]]