SAM - Revision history

Smith: /* Local Installation of R Server */

2015-01-27T22:35:41Z

‎Local Installation of R Server

2015-01-27T22:35:19Z

‎Local Installation of R Server

2014-10-15T18:03:17Z

‎Local Installation of R Server

2014-10-15T18:02:47Z

‎Local Installation of R Server

2014-04-22T19:10:52Z

‎Prerequisites

2014-01-13T16:05:59Z

‎Overview

2014-01-13T16:02:55Z

‎References

2014-01-13T16:01:59Z

‎Overview

2014-01-10T18:20:34Z

‎References

2014-01-10T18:19:04Z

‎References

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 ===Local Installation of R Server===
-The SAM analysis component can use a local installation of R on your desktop computer.  Please see [[Download_and_Installation#R_Installation_for_geWorkbench R Installation for geWorkbench]] for instructions.
+The SAM analysis component can use a local installation of R on your desktop computer.  Please see [[Download_and_Installation#R_Installation_for_geWorkbench |R Installation for geWorkbench]] for instructions.
 This has been tested with R versions 2.15.0 through 3.1.2.

@@ Line 19: / Line 19: @@
 ===Local Installation of R Server===
-The SAM analysis component can use a local installation of R on your desktop computer.
+The SAM analysis component can use a local installation of R on your desktop computer.  Please see [[Download_and_Installation#R_Installation_for_geWorkbench R Installation for geWorkbench]] for instructions.
-This has been tested with R versions 3.1.1, 3.0.3, 3.0.2 and 2.15.0.
+This has been tested with R versions 2.15.0 through 3.1.2.
 There are special considerations for installing R on Windows computers, please see [[Download_and_Installation#R_installation_on_Windows| R installation on Windows]].

@@ Line 21: / Line 21: @@
 The SAM analysis component can use a local installation of R on your desktop computer.
-This has been tested with R version 3.1.1, 3.0.3, 3.0.2 and 2.15.0.
+This has been tested with R versions 3.1.1, 3.0.3, 3.0.2 and 2.15.0.
 There are special considerations for installing R on Windows computers, please see [[Download_and_Installation#R_installation_on_Windows| R installation on Windows]].

@@ Line 21: / Line 21: @@
 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.
+This has been tested with R version 3.1.1, 3.0.3, 3.0.2 and 2.15.0.
 There are special considerations for installing R on Windows computers, please see [[Download_and_Installation#R_installation_on_Windows| R installation on Windows]].
@@ Line 27: / Line 27: @@
 Setting the R location in geWorkbench is covered at [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29| Preferences: R Location]].
+The following packages, if not already installed, will be downloaded and installed to the local R package directory:
 ===Prerequisites===

@@ Line 32: / Line 32: @@
 To use SAM in geWorkbench,
 # SAM must be loaded in the [[Component_Configuration_Manager| CCM]],
-# a gene expression dataset must be loaded in the Workspace,
+# a gene expression dataset must be loaded in the [[Workspace]],
 # "case" and "control" array sets must be activated in the Arrays component, and the case array sets designated as "case" (the default set type is "control").

@@ Line 5: / Line 5: @@
 ==SAM - Significance Analysis of Microarrays==
 ===Overview===
-SAM (Tusher et al., 2001) as implemented in geWorkbench evaluates the difference, for each gene, between its t-statistic for differential expression and that of a value obtained through permutations.  If the difference exceeds the "Delta" value, the expression is deemed significant.  The calculation can be repeated for different values of "Delta".  The user can set the step size between successive values of "Delta", and a maxiumum value.  A False Discovery Rate (FDR) is calculated at each value of Delta.  Further information on using SAM is available in the [http://statweb.stanford.edu/~tibs/SAM/sam.pdf SAM Manual]
+SAM (Tusher et al., 2001) is used to test for significantly differentially expressed genes between two groups.  It evaluates the difference, for each gene, between its t-statistic for differential expression and that of a value obtained through permutations.  If the difference exceeds the "Delta" value, the expression is deemed significant.  The calculation can be repeated for different values of "Delta".  The user can set the step size between successive values of "Delta", and a maxiumum value.  A False Discovery Rate (FDR) is calculated at each value of Delta.  Further information on using SAM is available in the [http://statweb.stanford.edu/~tibs/SAM/sam.pdf SAM Manual]
 ===siggenes===

@@ Line 95: / Line 95: @@
 ==References==
-Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to
+* Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to
 the ionizing radiation response (2001) Proc Natl Acad Sci U S A. '''98'''(9):5116-21. [http://www.ncbi.nlm.nih.gov/pubmed/11309499 PubMed 11309499]
-[http://bioconductor.org/packages/2.0/bioc/html/siggenes.html siggenes] Vignette (manual).
+* [http://bioconductor.org/packages/2.0/bioc/html/siggenes.html siggenes] Vignette (manual).
-[http://www.bioconductor.org/packages/release/bioc/manuals/siggenes/man/siggenes.pdf siggenes] package documentation.
+* [http://www.bioconductor.org/packages/release/bioc/manuals/siggenes/man/siggenes.pdf siggenes] package documentation.
-[http://statweb.stanford.edu/~tibs/SAM/ SAM website]
+* [http://statweb.stanford.edu/~tibs/SAM/ SAM website]

@@ Line 96: / Line 96: @@
 Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to
-the ionizing radiation response (2001) Proc Natl Acad Sci U S A. '''98'''(9):5116-21
+the ionizing radiation response (2001) Proc Natl Acad Sci U S A. '''98'''(9):5116-21 [http://www.ncbi.nlm.nih.gov/pubmed/11309499 PubMed 11309499]
 [http://bioconductor.org/packages/2.0/bioc/html/siggenes.html siggenes] manual.