EMMAWiki/WebDocumentation/GeneralUsage/ImportDatafromArrayLIMS - Revision history

Alu: /* Step 6 Job Submitted */

2011-10-26T12:42:03Z

Step 6 Job Submitted

← Older revision		Revision as of 14:42, 26 October 2011
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	== Step 6 Job Submitted ==		== Step 6 Job Submitted ==
	This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the ~~[[EMMAWiki/WebDocumentation/~~ViewResults~~\|ViewResults]]~~ page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].		This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the ViewResults page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].

Alu: /* HowTo Import Data From the ArrayLIMS */

2011-10-26T12:40:21Z

HowTo Import Data From the ArrayLIMS

← Older revision		Revision as of 14:40, 26 October 2011
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	__NOTOC__		__NOTOC__
	<!-- ## page was renamed from [[ImportingData]] -->		<!-- ## page was renamed from [[ImportingData]] -->
	= [[HowTo]] Import Data From the ArrayLIMS =		= HowTo Import Data From the ArrayLIMS =

	This page describes how to import data from [[ArrayLIMSWiki\|ArrayLIMS]] to the [[EMMAWiki\|EMMA System]].		This page describes how to import data from [[ArrayLIMSWiki\|ArrayLIMS]] to the [[EMMAWiki\|EMMA System]].

Alu: /* HowTo Import Data From the ArrayLIMS */

2011-10-26T12:40:10Z

HowTo Import Data From the ArrayLIMS

← Older revision		Revision as of 14:40, 26 October 2011
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	To be able to import data to [[EMMAWiki\|EMMA]] one has to select an Experiment first or to create a new experiment in your project you might want to import data to it. All imported Arrays will be appended to the selected Experiment. After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.		To be able to import data to [[EMMAWiki\|EMMA]] one has to select an Experiment first or to create a new experiment in your project you might want to import data to it. All imported Arrays will be appended to the selected Experiment. After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.

	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~MainMenul.png]]		[[File:MainMenul.png]]

	Use this link to get to the main import page.		Use this link to get to the main import page.
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	Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLIMS]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLIMS]] Projects.		Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLIMS]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLIMS]] Projects.
	Now you have to select the one you want to import arrays from. If you see no project, you are not member of project. Ask your ArrayLIMS administrator for access.		Now you have to select the one you want to import arrays from. If you see no project, you are not member of project. Ask your ArrayLIMS administrator for access.
	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~import1.png]]		[[File:import1.png]]

	== Step 2 Select Slides ==		== Step 2 Select Slides ==

	After the project selection is done you have to select the slides you want to import. The list shows all slides available in the selected project and lists there slide names and optionally a type and some remarks. To be listed here the slides also have to contain valid images to be importable. Use the checkboxes to select one or more slides and continue with step 3.		After the project selection is done you have to select the slides you want to import. The list shows all slides available in the selected project and lists there slide names and optionally a type and some remarks. To be listed here the slides also have to contain valid images to be importable. Use the checkboxes to select one or more slides and continue with step 3.
	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~import1b.png]]		[[File:import1b.png]]

	* Note: This is an example. Which slides you actually see depends on your project.		* Note: This is an example. Which slides you actually see depends on your project.
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	In the following example, there are two channels, one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel" assignment you can continue to the next step, but don't be confused, it will take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large...		In the following example, there are two channels, one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel" assignment you can continue to the next step, but don't be confused, it will take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large...

	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~import2.png]]		[[File:import2.png]]

	* Note that if you have scanned more than one image per channel you will see four or more rows per slide.		* Note that if you have scanned more than one image per channel you will see four or more rows per slide.
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	After the data file parsing is done, you have to select a proper ArrayLayout for each slide. In the normal case there will just be one Layout listed and you just have to select this one. If the list contains more than one layout for a slide, you have to select the correct one used for your Experiment. If you try to import slides where EMMA does not list any layouts, you have to import the appropriate layout first before you can import the [[ArrayLIMSWiki\|ArrayLIMS]] slides according to the layout.		After the data file parsing is done, you have to select a proper ArrayLayout for each slide. In the normal case there will just be one Layout listed and you just have to select this one. If the list contains more than one layout for a slide, you have to select the correct one used for your Experiment. If you try to import slides where EMMA does not list any layouts, you have to import the appropriate layout first before you can import the [[ArrayLIMSWiki\|ArrayLIMS]] slides according to the layout.

	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~import3.png]]		[[File:import3.png]]

	== Step 5 Selection Overview ==		== Step 5 Selection Overview ==
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	and fix it, otherwise click the "Start Import" Button to submit the import job.		and fix it, otherwise click the "Start Import" Button to submit the import job.

	[[~~Image~~:~~EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$~~import4.png]]		[[File:import4.png]]

	== Step 6 Job Submitted ==		== Step 6 Job Submitted ==
	This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the [[EMMAWiki/WebDocumentation/ViewResults\|ViewResults]] page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].		This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the [[EMMAWiki/WebDocumentation/ViewResults\|ViewResults]] page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].

Admin: 4 revisions

2011-10-26T06:13:12Z

4 revisions

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

imported>VirginieMittard at 13:46, 5 September 2005

2005-09-05T13:46:00Z

← Older revision		Revision as of 15:46, 5 September 2005
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	== Step 3 Image Selection ==		== Step 3 Image Selection ==

	Here you have to select appropriate [[Image and data upload\|images]] from the selected slides and assign them to the channels. For each array you have selected in the previous step, select the channel assignment for each data file. If you have scanned with [[ImaGene]], you will select two files for each slide.		Here you have to select appropriate [[Image and data upload\|images]] from the selected slides and assign them to the channels. For each array you have selected in the previous step, select the channel assignment for each data file. If you have scanned with ImaGene, you will select two files for each slide.
	In the following example, there are two channels, one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel" assignment you can continue to the next step, but don't be confused, it will take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large...		In the following example, there are two channels, one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel" assignment you can continue to the next step, but don't be confused, it will take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large...

imported>VirginieMittard at 13:45, 5 September 2005

2005-09-05T13:45:19Z

← Older revision		Revision as of 15:45, 5 September 2005
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	= [[HowTo]] Import Data From the ArrayLIMS =		= [[HowTo]] Import Data From the ArrayLIMS =

	~~After you have created~~ a new experiment in your project you might want to import data to it. ~~Therefore please use~~ the ~~ImportWizzard~~.		This page describes how to import data from [[ArrayLIMSWiki\|ArrayLIMS]] to the [[EMMAWiki\|EMMA System]].
	~~Before you can import data you need~~ an ~~existing experiment. So either create one or use an existing one.~~		To be able to import data to [[EMMAWiki\|EMMA]] one has to select an Experiment first or to create a new experiment in your project you might want to import data to it. All imported Arrays will be appended to the selected Experiment. After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.

	* While you are working with the experiment, ~~you will find following navigation buttons on~~ the ~~left:~~

	[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$MainMenul.png]]		[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$MainMenul.png]]

	* Click on ''Import from ArrayLIMS''		Use this link to get to the main import page.
	~~------~~
	* You will see the ~~following screen:~~
	Just follow the instructions at the top. It will guide you through a six step process.		Just follow the instructions at the top. It will guide you through a six step process.
	* Select the appropriate ArrayLIMS ~~project~~. If you see no project, you are not member of project. Ask your ArrayLIMS administrator for access.
			== Step 1 Select an ArrayLIMS Project ==

			Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLIMS]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLIMS]] Projects.
			Now you have to select the one you want to import arrays from. If you see no project, you are not member of project. Ask your ArrayLIMS administrator for access.
	[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import1.png]]		[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import1.png]]

	~~------~~		== Step 2 Select Slides ==
	* Select one or many slides ~~from the arraylims~~ you want to import:
			After the project selection is done you have to select the slides you want to import. The list shows all slides available in the selected project and lists there slide names and optionally a type and some remarks. To be listed here the slides also have to contain valid images to be importable. Use the checkboxes to select one or more slides and continue with step 3.
	[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import1b.png]]		[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import1b.png]]

	* Note: This is an example. Which slides you actually see depends on your project.		* Note: This is an example. Which slides you actually see depends on your project.
	~~------~~
	* For each array you have selected in the previous step, select the channel assignment for each data file. Be careful to select the correct channel for each slide.
	* If you have scanned more than one image per channel you will see four or more rows per slide
	* Select two files for each slide. If you select one on the left the corresponding image on the right will be highlighted.
	~~[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import2.png]]~~
	~~------~~
	* Select the appropriate [[ArrayLayout]] for this slide. Normally only one will fit each slide, but you have to select it anyway.
	~~[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import3.png]]~~
	~~------~~
	* Check your settings and enter an appropriate common name for your slides:

	[[Image~~:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import4.png]]~~		== Step 3 Image Selection ==

	~~= Import Data~~ from ArrayLIMS =		Here you have to select appropriate [[Image and data upload\|images]] from the selected slides and assign them to the channels. For each array you have selected in the previous step, select the channel assignment for each data file. If you have scanned with [[ImaGene]], you will select two files for each slide.
			In the following example, there are two channels, one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel" assignment you can continue to the next step, but don't be confused, it will take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large...

	~~This page describes how to import data from [[ArrayLIMSWiki\|ArrayLIMS]] to the~~ [[EMMAWiki~~\|EMMA System]]~~.		[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import2.png]]
	~~To be able to import data to [[EMMAWiki\|EMMA~~]] ~~one has to select an Experiment first. All imported Arrays will~~
	~~be appended to the selected Experiment.~~
	~~After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.~~
	~~Use this link to get to the main import page.~~

	~~The ArrayLIMS import is devided into 6 steps.~~

	~~== Step 1 Select an ArrayLIMS Project ==~~		* Note that if you have scanned more than one image per channel you will see four or more rows per slide.
	~~Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLIMS]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLIMS]] Projects.~~
	~~Now you have to select the one you want to import arrays from.~~

	~~== Step 2 Select Slides ==~~
	~~After the project selection is done you have to select the slides~~ you ~~want to import. The list shows all slides available in the selected project and lists there slide names and optionally a type and some remarks. To be listed here the slides also~~ have ~~to contain valid images to be importable. Use the checkboxes to select one or~~ more ~~slides and continue with step 3.~~

	~~== Step 3 Image Selection ==~~
	~~Here you have to select appropriate [[Image and data upload\|images]] from the selected slides and assign them to the channels. There are two channels,~~ one for the "Experiment" (the first channel) and one for "Control" (the second channel). Each [[ArrayLIMSWiki\|ArrayLIMS]] Slide contains two [[Image and data upload\|images]] and now you have to assign the [[Image and data upload\|images]] to the channels, that is, choose one [[Image and data upload\|images]] for channel one and the other [[Image and data upload\|images]] for channel two. The [[ArrayLIMSWiki\|ArrayLIMS]] System tells you which color marker is used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assign the correct [[Image and data upload\|images]] to the channels, just be careful not to switch on channels if you don't want to. After the "image to channel~~" assignment~~ you ~~can continue to the next step, but don't be confused, it~~ will ~~take a while until the "Step 4" page is loaded, because we have to parse the appropriate data files and count the spot information and the files are quite large..~~.

	== Step 4 Choose [[ArrayLayout]] ==		== Step 4 Choose [[ArrayLayout]] ==
	After the data file parsing is done, you have to select a proper ArrayLayout for each slide. In the normal case there will just be one Layout listed and you just have to select this one. If the list contains more than one layout for a slide, you have to select the correct one used for your Experiment. If you try to import slides where EMMA does not list any layouts, you have to import the appropriate layout first before you can import the [[ArrayLIMSWiki\|ArrayLIMS]] slides according to the layout.		After the data file parsing is done, you have to select a proper ArrayLayout for each slide. In the normal case there will just be one Layout listed and you just have to select this one. If the list contains more than one layout for a slide, you have to select the correct one used for your Experiment. If you try to import slides where EMMA does not list any layouts, you have to import the appropriate layout first before you can import the [[ArrayLIMSWiki\|ArrayLIMS]] slides according to the layout.

			[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import3.png]]

	== Step 5 Selection Overview ==		== Step 5 Selection Overview ==
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	to verify that all data are correct before you start the import.If you find a mistake in the selected data, please use your browser's back button		to verify that all data are correct before you start the import.If you find a mistake in the selected data, please use your browser's back button
	and fix it, otherwise click the "Start Import" Button to submit the import job.		and fix it, otherwise click the "Start Import" Button to submit the import job.

			[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLIMS$import4.png]]

	== Step 6 Job Submitted ==		== Step 6 Job Submitted ==
	This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the [[EMMAWiki/WebDocumentation/ViewResults\|ViewResults]] page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].		This is just an information page that tells you that the import job was successfully submitted and is running now. To view the status of the job, you can use the [[EMMAWiki/WebDocumentation/ViewResults\|ViewResults]] page reachable from the [[EMMAWiki/WebDocumentation/BasicMenu\|BasicMenu]].

imported>VirginieMittard at 13:23, 5 September 2005

2005-09-05T13:23:45Z

@@ Line 1: / Line 1: @@
 __NOTOC__
 = [[HowTo]] Import Data From the ArrayLIMS =
-After you have created a new experiment in your project you might want to data to it. Therefor please use the ImportWizzard.
+After you have created a new experiment in your project you might want to import data to it. Therefore please use the ImportWizzard.

Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= [[HowTo]] Import Data From the ArrayLIMS =

After you have created a new experiment in your project you might want to data to it. Therefor please use the ImportWizzard.