EMMAWiki/WebDocumentation/GeneralUsage/AnalyseArrays - Revision history

Alu: /* Advanced options */

2011-10-26T12:48:17Z

Advanced options

← Older revision		Revision as of 14:48, 26 October 2011
Line 29:		Line 29:
	\|colspan="3" < >\|'''Parameter adjustment and individual configuration:'''		\|colspan="3" < >\|'''Parameter adjustment and individual configuration:'''
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~selectarrays.png]]		\| [[File:selectarrays.png]]
	\| Click the "Select Arrays"-Button to specify the arrays or hybridizations, respectively, you want to include.		\| Click the "Select Arrays"-Button to specify the arrays or hybridizations, respectively, you want to include.
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~factorbrowserselect.png]]		\| [[File:factorbrowserselect.png]]
	\| Choose your arrays by clicking on the checkboxes next to array names. And finally return to the analysis pipeline by clicking on the basic action "Select & Return".		\| Choose your arrays by clicking on the checkboxes next to array names. And finally return to the analysis pipeline by clicking on the basic action "Select & Return".
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~advanced.png]]		\| [[File:advanced.png]]
	\| On the right side of the Analysis Arrays page, there's an option to show advanced configuration and data selection dialogs.		\| On the right side of the Analysis Arrays page, there's an option to show advanced configuration and data selection dialogs.
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~advancedoverview.png]]		\| [[File:advancedoverview.png]]
	\| These advanced options give you the possibility to fine-tune your analysis pipeline.		\| These advanced options give you the possibility to fine-tune your analysis pipeline.
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~configuretools.png]]		\| [[File:configuretools.png]]
	\| After selecting the "Configure Tool"-Option you will see the functions your pipeline consists of. By clicking on a function name, a new window will open, which allows further parameter adjustments.		\| After selecting the "Configure Tool"-Option you will see the functions your pipeline consists of. By clicking on a function name, a new window will open, which allows further parameter adjustments.
	\|-		\|-
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~configoptions.png]]		\| [[File:configoptions.png]]
	\| Adjust the parameters of the selected function. This example shows the configuration of the Significance Test. So you could for instance change from the default setting "t.test" to "wilcox.test" significance test.		\| Adjust the parameters of the selected function. This example shows the configuration of the Significance Test. So you could for instance change from the default setting "t.test" to "wilcox.test" significance test.

Alu: /* A short introduction */

2011-10-26T12:47:42Z

A short introduction

← Older revision		Revision as of 14:47, 26 October 2011
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	\|-		\|-
	\| '''3.'''		\| '''3.'''
	\| [[File:~~AnalyseArrays$~~compute.png]]		\| [[File:compute.png]]
	\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed		\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed
	\|}		\|}

Alu: /* A short introduction */

2011-10-26T12:47:22Z

A short introduction

← Older revision		Revision as of 14:47, 26 October 2011
Line 10:		Line 10:
	\|-		\|-
	\| '''1.'''		\| '''1.'''
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~startanalysis.png]]		\| [[File:startanalysis.png]]
	\| Start to analyze your arrays by clicking on the link in the Basic Actions menu in the experiment overview		\| Start to analyze your arrays by clicking on the link in the Basic Actions menu in the experiment overview
	\|-		\|-
	\| '''2.'''		\| '''2.'''
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~choosemethod2.png]]		\| [[File:choosemethod2.png]]
	\| At first you have to select the analysis method you want to perform, e.g. Normalization or Significance Test		\| At first you have to select the analysis method you want to perform, e.g. Normalization or Significance Test
	\|-		\|-
	\| '''3.'''		\| '''3.'''
	\| [[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$~~AnalyseArrays$compute.png]]		\| [[File:AnalyseArrays$compute.png]]
	\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed		\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed
	\|}		\|}

Admin: 11 revisions

2011-10-26T06:15:45Z

11 revisions

← Older revision	Revision as of 08:15, 26 October 2011
(No difference)

imported>VirginieMittard at 13:53, 25 August 2005

2005-08-25T13:53:26Z

← Older revision		Revision as of 15:53, 25 August 2005
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	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advancedoverview.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advancedoverview.png]]
	\| These advanced options give you the possibility to fine tune your analysis pipeline.		\| These advanced options give you the possibility to fine-tune your analysis pipeline.
	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configuretools.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configuretools.png]]

imported>VirginieMittard at 13:53, 25 August 2005

2005-08-25T13:53:12Z

← Older revision		Revision as of 15:53, 25 August 2005
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	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configoptions.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configoptions.png]]
	\| Adjust the parameters of the selected function. This example shows the configuration of the Significance Test. So you could for instance change from the default setting "t.test" to "~~wilcoxon~~" significance test.		\| Adjust the parameters of the selected function. This example shows the configuration of the Significance Test. So you could for instance change from the default setting "t.test" to "wilcox.test" significance test.

imported>VirginieMittard at 13:50, 25 August 2005

2005-08-25T13:50:38Z

← Older revision		Revision as of 15:50, 25 August 2005
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	== Synopsis ==		== Synopsis ==

	This page describes how you can ~~analyse~~ your data. This is done in so called "pipelines". After reading this page, you will have understood how this works. In the beginning ~~there's~~ a short ~~overview~~ about ~~the analyse~~. This introduces the basic concepts. Afterwards ~~there are explained~~ some more details, like ~~the~~ parameter adjustment and function configuration.		This page describes how you can analyze your data. This is done in so called "pipelines". After reading this page, you will have understood how this works. In the beginning we give a short presentation about how to start an analysis of your arrays. This introduces the basic concepts. Afterwards we explain some more details about the pipeline application, like parameter adjustment and function configuration.

	== A short introduction ==		== A short introduction ==

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\|colspan="3" < >\| '''~~Analyse~~ Arrays - the easy way:'''		\|colspan="3" < >\| '''Analyze Arrays - the easy way:'''
	\|-		\|-
	\| '''1.'''		\| '''1.'''
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$startanalysis.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$startanalysis.png]]
	\| Start to ~~analyse~~ your arrays by clicking on the link in the Basic Actions menu in the experiment overview		\| Start to analyze your arrays by clicking on the link in the Basic Actions menu in the experiment overview
	\|-		\|-
	\| '''2.'''		\| '''2.'''
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$~~choosemethod~~.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$choosemethod2.png]]
	\| At first you have to select the analysis method you want to perform, e.g. Normalization or Significance Test		\| At first you have to select the analysis method you want to perform, e.g. Normalization or Significance Test
	\|-		\|-
Line 24:		Line 24:
	== Advanced options ==		== Advanced options ==

	Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, respectively, you want to include in your ~~analyse~~, and ends with the configuration of the functions, each pipeline consists of.		Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, respectively, you want to include in your analysis, and ends with the configuration of the functions, each pipeline consists of.

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
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	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advanced.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advanced.png]]
	\| On the right side of the ~~Analyse~~ Arrays page, there's an option to show advanced configuration and data selection dialogs.		\| On the right side of the Analysis Arrays page, there's an option to show advanced configuration and data selection dialogs.
	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advancedoverview.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advancedoverview.png]]

imported>StefanAlbaum at 14:06, 18 April 2005

2005-04-18T14:06:59Z

← Older revision		Revision as of 16:06, 18 April 2005
Line 1:		Line 1:
	__NOTOC__		__NOTOC__
			== Synopsis ==

			This page describes how you can analyse your data. This is done in so called "pipelines". After reading this page, you will have understood how this works. In the beginning there's a short overview about the analyse. This introduces the basic concepts. Afterwards there are explained some more details, like the parameter adjustment and function configuration.

			== A short introduction ==

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\|colspan="3" < >\|'''Analyse Arrays - the easy way:'''		\|colspan="3" < >\| '''Analyse Arrays - the easy way:'''
	\|-		\|-
	\| '''1.'''		\| '''1.'''
Line 15:		Line 21:
	\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed		\| Now you can just hit the "Compute and View Results"-Button and your selected analysis pipeline will be performed
	\|}		\|}

			== Advanced options ==

	Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, respectively, you want to include in your analyse, and ends with the configuration of the functions, each pipeline consists of.		Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, respectively, you want to include in your analyse, and ends with the configuration of the functions, each pipeline consists of.

imported>StefanAlbaum at 13:36, 18 April 2005

2005-04-18T13:36:10Z

← Older revision		Revision as of 15:36, 18 April 2005
Line 37:		Line 37:
	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configoptions.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configoptions.png]]
	\| Adjust the parameters of the selected function.		\| Adjust the parameters of the selected function. This example shows the configuration of the Significance Test. So you could for instance change from the default setting "t.test" to "wilcoxon" significance test.

imported>StefanAlbaum at 13:00, 18 April 2005

2005-04-18T13:00:58Z

← Older revision		Revision as of 15:00, 18 April 2005
Line 16:		Line 16:
	\|}		\|}

	Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, ~~respectivly~~, you want to include in your analyse, and ends with the configuration of the functions, each pipeline consists of.		Further on, there are of course a lot of adjustable parameters. This begins by the number of arrays or hybridizations, respectively, you want to include in your analyse, and ends with the configuration of the functions, each pipeline consists of.

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
Line 22:		Line 22:
	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$selectarrays.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$selectarrays.png]]
	\| Click the "Select Arrays"-Button to specify the arrays or hybridizations, ~~respectivly~~, you want to include.		\| Click the "Select Arrays"-Button to specify the arrays or hybridizations, respectively, you want to include.
	\|-		\|-
	\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$factorbrowserselect.png]]		\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$factorbrowserselect.png]]
	\| Choose your arrays by clicking on the checkboxes next to array names. And finally return to the analysis pipeline by clicking on the basic action "Select & Return"		\| Choose your arrays by clicking on the checkboxes next to array names. And finally return to the analysis pipeline by clicking on the basic action "Select & Return".
			\|-
			\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advanced.png]]
			\| On the right side of the Analyse Arrays page, there's an option to show advanced configuration and data selection dialogs.
			\|-
			\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$advancedoverview.png]]
			\| These advanced options give you the possibility to fine tune your analysis pipeline.
			\|-
			\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configuretools.png]]
			\| After selecting the "Configure Tool"-Option you will see the functions your pipeline consists of. By clicking on a function name, a new window will open, which allows further parameter adjustments.
			\|-
			\| [[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$AnalyseArrays$configoptions.png]]
			\| Adjust the parameters of the selected function.