Normalization - Revision history

Smith: /* Overview */

2014-04-22T20:38:18Z

‎Overview

2014-04-22T20:37:50Z

‎Overview

2013-10-16T21:49:20Z

‎Overview

2013-10-16T21:48:49Z

‎Overview

2013-07-16T18:38:08Z

‎Housekeeping Genes Normalizer

2013-07-16T18:37:46Z

‎Normalizer Configuration

2012-03-01T17:20:54Z

‎Normalizer Configuration

2012-03-01T17:17:24Z

‎Overview

2012-03-01T17:15:01Z

‎Overview

2012-03-01T17:14:03Z

‎Overview

← Older revision		Revision as of 20:38, 22 April 2014
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	Data preparation methods such as RMA and GCRMA are not directly available in geWorkbench. Affymetrix CEL files can be processed externally to geWorkbench using a program such as RMAExpress or in R/Bioconductor and then the processed data imported into geWorkbench.		Data preparation methods such as RMA and GCRMA are not directly available in geWorkbench. Affymetrix CEL files can be processed externally to geWorkbench using a program such as RMAExpress or in R/Bioconductor and then the processed data imported into geWorkbench.
−
−	~~A short introduction to various methods of Affymetrix data preparation is available at [http://discover.nci.nih.gov/microarrayAnalysis/Affymetrix.Preprocessing.jsp Affymetrix Preprocessing].~~

	The Normalization dialogs can be reached in two ways, either directly from the [[Workspace]] by a right-click menu on a microarray dataset,		The Normalization dialogs can be reached in two ways, either directly from the [[Workspace]] by a right-click menu on a microarray dataset,

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 A short introduction to various methods of Affymetrix data preparation is available at [http://discover.nci.nih.gov/microarrayAnalysis/Affymetrix.Preprocessing.jsp Affymetrix Preprocessing].
-The Normalization dialogs can be reached in two ways, either directly from the Workspace by a right-click menu on a microarray dataset,
+The Normalization dialogs can be reached in two ways, either directly from the [[Workspace]] by a right-click menu on a microarray dataset,
 [[Image:Workspace_Data_Normalization.png]]

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 =Overview=
-Normalization is used to transform data in preparation for analysis.  Many normalizers are oriented towards decreasing the effects of systematic differences across a set of microarrays, aiding in cross-microarray comparisons.  A log transformation of the data can be used to improve its statistical distribution.  geWorkbench offers a selection of pluggable normalization components (see list below).  The Normalizer panel is located in the <b>Commands and Analysis</b> area in the lower right side of the application.
+Normalization is used to transform data in preparation for analysis.  Many normalizers are oriented towards decreasing the effects of systematic differences across a set of microarrays, aiding in cross-microarray comparisons.  A log transformation of the data can be used to improve its statistical distribution.  geWorkbench offers a selection of pluggable normalization components (see list below).
 All normalization operations directly alter the loaded data set and are not reversible. A separate copy of the data is not generated. Normalization operations do not respect any marker or array sets that may be activated; normalization always acts on the entire data set.

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 A short introduction to various methods of Affymetrix data preparation is available at [http://discover.nci.nih.gov/microarrayAnalysis/Affymetrix.Preprocessing.jsp Affymetrix Preprocessing].
-As of geWorkbench 2.3.0, all normalizers are activated in one of two ways:
+The Normalization dialogs can be reached in two ways, either directly from the Workspace by a right-click menu on a microarray dataset,
-This is depicted for the Project Folders component
+[[Image:Workspace_Data_Normalization.png]]
-[[Image:Project_Folders_Normalization_Menu.png]]
+or through the top Menu Bar Commands->Normalization menu, which will bring up the same choices.
 =Normalizer Configuration=

← Older revision		Revision as of 18:38, 16 July 2013
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	==Housekeeping Genes Normalizer==		==Housekeeping Genes Normalizer==

−	[[Image:Normalization-HouseKeeping.png]]	+	[[Image:Normalization-HouseKeeping.png\|{{ImageMaxWidth}}]]

← Older revision		Revision as of 18:37, 16 July 2013
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−	[[Image:Normalizers_in_CCM.png]]	+	[[Image:Normalizers_in_CCM.png\|{{ImageMaxWidth}}]]

	=Available Normalizers=		=Available Normalizers=

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 =Normalizer Configuration=
-Some normalizers may not be loaded by default in geWorkbench.  To configure which normalizers to load, use the [[Tutorial_-_Component_Configuration_Manager| Component Configuration Manager]].  It is available in the top menu-bar under  '''Tools->Component Configuration'''.
+Some normalizers may not be loaded by default in geWorkbench.  To configure which normalizers to load, use the [[Component_Configuration_Manager| Component Configuration Manager]].  It is available in the top menu-bar under  '''Tools->Component Configuration'''.
 [[Image:Normalizers_in_CCM.png]]

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 ==Overview==
 See any of the below normalizers for a depiction of these controls.
 * '''Saved Parameters''' (menu) - Allows selection of stored parameter settings.
 * '''Normalize''' (button)- Run the selected transformation.
 * '''Save Settings''' - Save the current settings (see following section).
 * '''Delete Settings'''- Delete the currently selected parameter set.