Difference between revisions of "SAM"

(Local Installation of R Server)
(Local Installation of R Server)
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This has been tested with R version 2.15.0 and 3.0.2.
 
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 [[Download_and_Installation#R_installation_on_Windows| R installation on Windows]].
  
If a local installation is used, you must set the R Location in the geWorkbench Preferences menu, as shown below:
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Setting the R location in geWorkbench is covered at [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29| Preferences: R Location]].
 
 
 
 
[[Image:SAM_R_Location.png]]
 
 
 
For special details on installing R under Windows, please see [[Download_and_Installation#R_installation | R Installation for Windows]].
 
 
 
 
 
Apple Macintosh users should install R in the usual default directory "Application". Since this is the default directory, the path to the R package directory can be left empty. However, the path to the Rscript location becomes, e.g.: /Library/Frameworks/R.framework/Versions/2.15/Resources/Rscript
 
 
 
[[Image:SAM_R_Location_Mac.png]]
 

Revision as of 17:45, 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



SAM - Significance Analysis of Microarrays

Local Installation of R Server

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.