Viper Analysis - Revision history

Smith: /* Parameters */

2015-02-10T22:34:44Z

‎Parameters

Smith: /* Parameters */

2015-02-10T22:33:05Z

‎Parameters

Smith: /* Prerequistes */

2015-01-27T22:51:39Z

‎Prerequistes

Smith: /* Prerequistes */

2015-01-27T22:51:11Z

‎Prerequistes

Smith: /* Parameters */

2013-12-18T22:11:13Z

‎Parameters

Smith at 22:08, 18 December 2013

2013-12-18T22:08:27Z

Smith at 23:24, 22 November 2013

2013-11-22T23:24:41Z

Smith: /* References */

2013-11-22T23:23:51Z

‎References

Smith at 22:36, 22 November 2013

2013-11-22T22:36:27Z

Smith: /* Data */

2013-11-22T22:30:23Z

‎Data

@@ Line 30: / Line 30: @@
 * '''Select Service'''
-** '''Local Service''' - run VIPER on an instance of R installed on the same machine as geWorkbench.
+** '''Local Service''' - Run VIPER on an instance of R installed on the same machine as geWorkbench.
-** '''Web service''' - not yet implemented.  Run Viper on a remote server.
+** '''Web service''' -  Run Viper on a remote server (local is recommended).
 * '''Select Regulon'''

@@ Line 40: / Line 40: @@
 * '''Select Method'''
 ** '''none''' - use if the data is already in rank format.
-** '''scale''' - for each gene (row in dataset), calculate the mean and standard deviation across all columns, then subtract the mean from each value in the row, and divide each by the standard deviation.
+** '''scale''' - for each gene (row in dataset), calculate the mean and standard deviation across all columns, then subtract the mean from each value in the row, and divide each by the standard deviation.  This assumes the data has a normal distribution, i.e. that it has already been log2 normalized.
 ** '''rank''' - rank transform row-wise
 ** '''mad''' - for each row, subtract the median, divide by the mean absolute deviation (MAD)

@@ Line 13: / Line 13: @@
 The local version of VIPER requires that R be installed on the same machine as geWorkbench.  Please see the R installation instructions on the [[Download_and_Installation|Download and Installation]] page.  The R location must then be set in the geWorkbench [[Preferences|Preferences]].
-'''Note''' - The version of Viper used in geWorkbench differs slightly from the freestanding version available in Bioconductor.  If you plan to run both versions on your machine, please set a separate package directory for R packages in geWorkbench in the [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29 Preferences]].  The geWorkbench version of Viper will be downloaded automatically to this directory on demand.
+'''Note''' - The version of Viper used in geWorkbench differs slightly from the freestanding version available in Bioconductor.  If you plan to run both versions on your machine, please set a separate package directory for R packages in geWorkbench in the [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29 |Preferences]].  The geWorkbench version of Viper will be downloaded automatically to this directory on demand.
 ==Data==

← Older revision		Revision as of 22:51, 27 January 2015
Line 13:		Line 13:
	The local version of VIPER requires that R be installed on the same machine as geWorkbench. Please see the R installation instructions on the [[Download_and_Installation\|Download and Installation]] page. The R location must then be set in the geWorkbench [[Preferences\|Preferences]].		The local version of VIPER requires that R be installed on the same machine as geWorkbench. Please see the R installation instructions on the [[Download_and_Installation\|Download and Installation]] page. The R location must then be set in the geWorkbench [[Preferences\|Preferences]].

		+	'''Note''' - The version of Viper used in geWorkbench differs slightly from the freestanding version available in Bioconductor. If you plan to run both versions on your machine, please set a separate package directory for R packages in geWorkbench in the [[Preferences#R_Location_.28Rscript.exe_and_its_folder.29 Preferences]]. The geWorkbench version of Viper will be downloaded automatically to this directory on demand.

	==Data==		==Data==

@@ Line 41: / Line 41: @@
 ** '''scale''' - for each gene (row in dataset), calculate the mean and standard deviation across all columns, then subtract the mean from each value in the row, and divide each by the standard deviation.
 ** '''rank''' - rank transform row-wise
-** '''mad''' - subtract the median, divide by the mean absolute deviation (MAD)
+** '''mad''' - for each row, subtract the median, divide by the mean absolute deviation (MAD)
-** '''ttest''' - for each gene, perform a t-test comparing each sample (column) one-at-a-time against all other samples taken together.
+** '''ttest''' - for each row, perform a t-test comparing each sample (column) one-at-a-time against all other samples taken together.
 ==References==
 <span id="Alvarez"></span>
 Mariano Alvarez Yao Shen, B. Belinda Ding, B. Hilda Ye and Andrea Califano, manuscript in preparation.

@@ Line 2: / Line 2: @@
 The '''VIPER''' (Virtual Inference of Protein-activity by Enriched Regulon analysis) [[#Alvarez| [Alvarez et al., manuscript in preparation]]]
-component in geWorkbench transforms the expression profile for each sample (column) into a transcription-factor activity profile.  The activity of each transcription factor is inferred from that of its targets, where the targets are obtained from a cell-context-specific interaction network (interactome).  Three cell-context-specific interactomes are supplied, for leukemia, breast cancer, and prostate cancer.
+component in geWorkbench transforms the expression profile for each sample (column) into a transcription-factor activity profile, representing the relative activity of each TF in each sample.  The activity of each transcription factor is inferred from that of its targets, where the targets are obtained from a cell-context-specific interaction network (interactome).  Three cell-context-specific interactomes are supplied, for leukemia, breast cancer, and prostate cancer.
 The full standalone version of VIPER can also be downloaded from http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/VIPER.  VIPER is implemented in R and the standalone package has a number of additional functions which are documented in the [http://wiki.c2b2.columbia.edu/califanolab/images/0/08/Viper.pdf VIPER R vignette].
@@ Line 15: / Line 15: @@
 ==Data==
-VIPER requires expression data that is already in a form where the values for each sample are relative to a control value.  Each sample may represent e.g. the result of a drug perturbation.
+Individual samples may represent e.g. case and control experiments, or may all belong to a single type, e.g. drug perturbation experiments.  See the analysis method options for appropriate handling of different data types.
 ==Analysis==
 For a typical dataset containing expression values relative to control, the "Scale" method of analysis is recommended.
-VIPER analysis transforms the input expression matrix into a transcription factor activity matrix.  This matrix can be viewed in the Tabular Microarray Viewer, the Color Mosaic Viewer, or can be analyzed further e.g. with hierarchical clustering.
+VIPER analysis transforms the input expression matrix into a transcription factor activity matrix, representing the relative activity of each TF in each sample.  This matrix can be viewed in the Tabular Microarray Viewer, the Color Mosaic Viewer, or can be analyzed further e.g. with hierarchical clustering.
 ==Parameters==

← Older revision		Revision as of 23:23, 22 November 2013
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	==References==		==References==
−	Alvarez ~~et al~~, manuscript in preparation.	+	<span id="Alvarez"></span>
		+	Mariano Alvarez Yao Shen, B. Belinda Ding, B. Hilda Ye and Andrea Califano, manuscript in preparation.