ANOVA - Revision history

Smith at 22:21, 17 March 2015

2015-03-17T22:21:06Z

Smith: /* P-value corrections */

2015-03-12T19:59:35Z

‎P-value corrections

Smith at 16:38, 11 March 2015

2015-03-11T16:38:15Z

Smith: /* Overview */

2015-03-11T16:36:36Z

‎Overview

Smith: /* Overview */

2015-03-11T16:34:47Z

‎Overview

Smith: /* Prerequisites */

2015-03-11T15:06:29Z

‎Prerequisites

Smith: /* Prerequisites */

2015-03-10T20:43:10Z

‎Prerequisites

Smith: /* Prerequisites */

2015-03-10T20:42:16Z

‎Prerequisites

Smith: /* P-value corrections */

2014-11-03T21:21:08Z

‎P-value corrections

Smith: /* Overview */

2014-04-15T19:52:54Z

‎Overview

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 =Services (Grid)=
-ANOVA can be run either locally within geWorkbench, or remotely as a grid job on caGrid.  See the [[Tutorial_-_Grid_Services | Grid Services]] section for further details on setting up a grid job.
+ANOVA can be run either locally within geWorkbench, or remotely as a grid job on caGrid.  See the [[Grid_Services | Grid Services]] section for further details on setting up a grid job.
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 Columns represent individual arrays, and each row represents a marker.  The arrays are grouped by the array set to which they belong, with each set labeled at the top of the picture.  The markers are initially sorted in order of the calculated p-value, from smallest to largest.  The p-values are shown at right in the diagram.  Further details are available in the  [[Color_Mosaic |Color Mosaic tutorial]].
-The heat map depicted below was drawn using the "Relative" setting in the [[Tutorial_-_Viewing_a_Microarray_Dataset#Preferences | main Tools->Preferences->Visualization menu]].
+The heat map depicted below was drawn using the "Relative" setting in the [[Viewing_a_Microarray_Dataset#Preferences | main Tools->Preferences->Visualization menu]].
 * Note - In the Color Mosaic display of ANOVA results, the "Sort" button has no effect.  The "Sort" button is used only for the t-test, where it switches between ordering results by p-value and by fold-change.
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 ==Loading and preparing the example data==
-# Load the Bcell-100.exp dataset into geWorkbench as type "Affymetrix File Matrix".  (See [[Tutorial_-_Local_Data_Files | Local Data Files]]).
+# Load the Bcell-100.exp dataset into geWorkbench as type "Affymetrix File Matrix".  (See [[Local_Data_Files | Local Data Files]]).
 # When prompted, and if desired, load the annotation file.
 # For this example, the data was subjected to threshold normalization with a minimum value of 1.0 followed by log2 normalization (See [[Normalization| Normalization]]).
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 ==Results==
-The result of running ANOVA is a list of markers which meet the specified significance criteria.  These markers are placed into a new set in the Markers component called "Significant Genes".  The results are also displayed in visual components as detailed above for the Tabular Viewer and the Color Mosaic Viewer  [[Tutorial_-_ANOVA#Viewing_ANOVA_Results | (Viewing ANOVA Results)]].
+The result of running ANOVA is a list of markers which meet the specified significance criteria.  These markers are placed into a new set in the Markers component called "Significant Genes".  The results are also displayed in visual components as detailed above for the Tabular Viewer and the Color Mosaic Viewer  [[ANOVA#Viewing_ANOVA_Results | (Viewing ANOVA Results)]].
 =References=

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 * '''Just Alpha''' - No correction is performed.
 * '''Standard Bonferroni''' - The cutoff value (alpha) is divided by the number of tests (genes) before being compared with the calculated p-values.
-* '''Adjusted Bonferroni''' - Similar to the Bonferroni correction, but for each successive P-value in a list of p-values sorted in increasing order, the divisor for alpha is decremented by one and then the result compared with the P-value.  The effect is to slightly reduce the stringency (increase the power) of the Bonferroni correction.  This is a step-down procedure.
+* '''Adjusted (step-down) Bonferroni''' - Similar to the Bonferroni correction, but for each successive P-value in a list of p-values sorted in increasing order, the divisor for alpha is decremented by one and then the result compared with the P-value.  The effect is to slightly reduce the stringency (increase the power) of the Bonferroni correction.  This is a step-down procedure.
 * '''Westfall-Young Step-Down''' - (Dudoit, 2003) Another step-down procedure which adjusts the critical value alpha using the Max T method. (This correction is only available when the permutation method is chosen for calculating p-values).

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 =Overview=
 The ANOVA (ANalysis of VAriance) algorithm (Zar, 1999) is used to determine whether any significant difference in the means exist in a dataset composed of three or more groups of experimental tests.
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 Those markers for which a significant difference is found are placed into a new set in the Markers component called "Significant Genes".  The results are also displayed in the Tabular Viewer and as a heat map in the Color Mosaic component.
 =Setting up an ANOVA run=

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 The geWorkbench ANOVA component implements a one-way analysis of variance calculation derived from [http://www.tm4.org/mev.html TIGR's MeV (MultiExperiment Viewer)] (Saeed, 2003).  At least three groups of arrays must be specified by defining and activating them in the Arrays/Phenotypes component.    For each chosen marker the routine determines if, at the specified level of significance, any difference in the mean exists in expression values between any of the groups (the null hypothesis is that there is no difference between the groups).  Several basic methods of multiple testing correction are offered.  The analysis does not indicate between which groups the difference is found, only that one exists.
-Those markers for which a significant difference is found are placed into a new set in the Markers component called "Significant Genes".  The results are also display as a heat map in the Color Mosaic component.
+Those markers for which a significant difference is found are placed into a new set in the Markers component called "Significant Genes".  The results are also displayed in the Tabular Viewer and as a heat map in the Color Mosaic component.
 =ANOVA in geWorkbench web=

← Older revision		Revision as of 16:34, 11 March 2015
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	Those markers for which a significant difference is found are placed into a new set in the Markers component called "Significant Genes". The results are also display as a heat map in the Color Mosaic component.		Those markers for which a significant difference is found are placed into a new set in the Markers component called "Significant Genes". The results are also display as a heat map in the Color Mosaic component.
		+
		+	=ANOVA in geWorkbench web=
		+	Please see [[ANOVA_web]] for ANOVA in geWorkbench web.

	=Setting up an ANOVA run=		=Setting up an ANOVA run=

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 ==Prerequisites==
-# (Optional) Obtain the annotation file for the HG-U95Av2 array type from the Affymetrix NetAffx website (http://www.affymetrix.com/analysis/index.affx). The name will be similar to "HG_U95Av2.na29.annot.csv", where na29 is the version number. Loading the annotation file associates gene names and other information with the Affymetrix probeset IDs (see the geWorkbench FAQ for details on obtaining these files).
+# (Optional) Obtain the annotation file for the HG-U95Av2 array type from the Affymetrix NetAffx website (http://www.affymetrix.com/analysis/index.affx). The name will be similar to "HG_U95Av2.na34.annot.csv", where na34 is the version number. Loading the annotation file associates gene names and other information with the Affymetrix probeset IDs (see the geWorkbench FAQ for details on obtaining these files).
 ==Loading and preparing the example data==

← Older revision		Revision as of 20:43, 10 March 2015
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	* To use the ANOVA routine, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].		* To use the ANOVA routine, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].
−	* At least three array sets must be already defined.	+	* At least three array sets must be already defined and activated in the [[Array_Sets \| Array Sets]] component.

← Older revision		Revision as of 20:42, 10 March 2015
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	* To use the ANOVA routine, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].		* To use the ANOVA routine, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].
−	* ~~ANOVA is found in the list of loaded analysis routines in the lower-right '''Commands''' quadrant of geWorkbench~~.	+	* At least three array sets must be already defined.