EMMAWiki/AdministratorDocumentation/ArraylayoutGuide - Revision history

Alu: /* Arraylayout Guidelines */

2011-10-28T13:23:29Z

Arraylayout Guidelines

← Older revision		Revision as of 15:23, 28 October 2011
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	== Synopsis ==		== Synopsis ==

	An Array layout describes the physical properties of a micorarray. ~~See these [[Media:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutOverview.pdf]] slides for a brief overview on the different terms used in EMMA.~~		An Array layout describes the physical properties of a micorarray. '''An arraylayout is essential for your microarray experiment.''' All further processing and analysis is based on the layout. A wrong layout leads to a wrong calculation! Without a valid layout you will be unable to import any data.
	'''An arraylayout is essential for your microarray experiment.''' All further processing and analysis is based on the layout. A wrong layout leads to a wrong calculation! Without a valid layout you will be unable to import any data.

	Making an Array layout available to EMMA is a two-step process:		Making an Array layout available to EMMA is a two-step process:

Alu at 13:23, 28 October 2011

2011-10-28T13:23:01Z

← Older revision		Revision as of 15:23, 28 October 2011
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	This graphic explains the most common terms used:		This graphic explains the most common terms used:

	[[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~arraydesign.png]]		[[File:arraydesign.png]]

	=== Hints ===		=== Hints ===
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	# open the ''Advanced Actions'' menu		# open the ''Advanced Actions'' menu
	# follow the link ''View arraylayouts'':		# follow the link ''View arraylayouts'':
	[[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~leftmenu.png]]		[[File:leftmenu.png]]
	3.#3 click ''Import new arraylayout'' in Basic Actions:		3.#3 click ''Import new arraylayout'' in Basic Actions:
	[[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~leftmenu1.png]]		[[File:leftmenu1.png]]
	4.#4 Fill out the fields in the following form:		4.#4 Fill out the fields in the following form:
	[[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~arraylayoutUpload1.png]]		[[File:arraylayoutUpload1.png]]

	<span style="font-size: x-large; color: red">!</span> Use the browse button to select the ADF on your local disc. You have to enter the mandatory information.		<span style="font-size: x-large; color: red">!</span> Use the browse button to select the ADF on your local disc. You have to enter the mandatory information.
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	5.#5 When done, press the ''Upload [[ArrayLayout]]'' Button. EMMA will upload and check your layout. Please wait.		5.#5 When done, press the ''Upload [[ArrayLayout]]'' Button. EMMA will upload and check your layout. Please wait.
	This will take a few minutes to proceed. Often you will see an error message like this: [[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~arraylayoutUpload2.png]].		This will take a few minutes to proceed. Often you will see an error message like this: [[File:arraylayoutUpload2.png]].

	This means something is wrong with your ADF. The message is rather clear in what it does not like. Please correct the errors in your file and try again.		This means something is wrong with your ADF. The message is rather clear in what it does not like. Please correct the errors in your file and try again.

	If you messed only with the physical layout information, EMMA corrects the values automatically from parsing your file. If the values in red are correct you may still proceed.		If you messed only with the physical layout information, EMMA corrects the values automatically from parsing your file. If the values in red are correct you may still proceed.
	[[~~Image~~:~~EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~arraylayoutUpload3.png]]		[[File:arraylayoutUpload3.png]]

	6.#6 You may review your settings. if everything is fine, click the ''Add to database'' button.		6.#6 You may review your settings. if everything is fine, click the ''Add to database'' button.
	This will create a background job that will add your layout permanently to your project. Follow the link to see the progress of your import. The import may take several hours. The [[ArrayLayout]] will be available only after it is finished.		This will create a background job that will add your layout permanently to your project. Follow the link to see the progress of your import. The import may take several hours. The [[ArrayLayout]] will be available only after it is finished.

Admin: 13 revisions

2011-10-26T06:13:09Z

13 revisions

← Older revision	Revision as of 08:13, 26 October 2011
(No difference)

imported>VirginieMittard at 11:30, 22 December 2006

2006-12-22T11:30:30Z

← Older revision		Revision as of 13:30, 22 December 2006
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	== Uploading the ADF ==		== Uploading the ADF ==

	# open the ''Advanced Actions'' ~~menue~~		# open the ''Advanced Actions'' menu
	# follow the link ''View arraylayouts'':		# follow the link ''View arraylayouts'':
	[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$leftmenu.png]]		[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$leftmenu.png]]

imported>MichaelDondrup at 18:25, 21 December 2006

2006-12-21T18:25:14Z

← Older revision		Revision as of 20:25, 21 December 2006
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	This graphic explains the most common terms used:		This graphic explains the most common terms used:

	[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$~~arraylayout~~.png]]		[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraydesign.png]]

	=== Hints ===		=== Hints ===

imported>MichaelDondrup at 18:20, 21 December 2006

2006-12-21T18:20:35Z

← Older revision		Revision as of 20:20, 21 December 2006
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	You need to have the role ''Chief'' or ''Maintainer'' within your project to be able to upload ADF-files to EMMA. So check with the Maintainer of your project, to see how to upload your ADF.		You need to have the role ''Chief'' or ''Maintainer'' within your project to be able to upload ADF-files to EMMA. So check with the Maintainer of your project, to see how to upload your ADF.

			This graphic explains the most common terms used:

			[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayout.png]]

	=== Hints ===		=== Hints ===

imported>MichaelDondrup at 09:30, 21 December 2006

2006-12-21T09:30:07Z

@@ Line 43: / Line 43: @@
 == Uploading the ADF ==
-* open the ''Advanced Options'' menue
+# open the ''Advanced Actions'' menue
-* follow the link ''View Arraylayouts''
+# follow the link ''View arraylayouts'':
-[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutUpload1.png]]
+If you messed only with the physical layout information, EMMA corrects the values automatically from parsing your file. If the values in red are correct you may still proceed.
 [[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutUpload3.png]]

imported>MichaelDondrup at 08:47, 21 December 2006

2006-12-21T08:47:37Z

← Older revision		Revision as of 10:47, 21 December 2006
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	* open the ''Advanced Options'' menue		* open the ''Advanced Options'' menue
	* follow the link ''View Arraylayouts''		* follow the link ''View Arraylayouts''

			[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutUpload1.png]]
			[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutUpload2.png]]
			[[Image:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutUpload3.png]]

imported>MichaelDondrup at 08:41, 21 December 2006

2006-12-21T08:41:11Z

← Older revision		Revision as of 10:41, 21 December 2006
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	== Uploading the ADF ==		== Uploading the ADF ==

			* open the ''Advanced Options'' menue
			* follow the link ''View Arraylayouts''

imported>MichaelDondrup at 11:04, 18 December 2006

2006-12-18T11:04:19Z

← Older revision		Revision as of 13:04, 18 December 2006
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	== Synopsis ==		== Synopsis ==

	An Array layout describes the physical properties of a micorarray. See these pdf-slides for a brief overview on the different terms used in EMMA.		An Array layout describes the physical properties of a micorarray. See these [[Media:EMMAWiki$$AdministratorDocumentation$$ArraylayoutGuide$arraylayoutOverview.pdf]] slides for a brief overview on the different terms used in EMMA.
	'''An arraylayout is essential for your microarray experiment.''' All further processing and analysis is based on the layout. A wrong layout leads to a wrong calculation! Without a valid layout you will be unable to import any data.		'''An arraylayout is essential for your microarray experiment.''' All further processing and analysis is based on the layout. A wrong layout leads to a wrong calculation! Without a valid layout you will be unable to import any data.