EMMAWiki/WebDocumentation/GeneralUsage/ImportDatafromArrayLims - Revision history

Admin: 38 revisions

2011-10-26T06:16:33Z

38 revisions

← Older revision	Revision as of 08:16, 26 October 2011
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imported>VirginieMittard at 13:19, 5 September 2005

2005-09-05T13:19:23Z

← Older revision		Revision as of 15:19, 5 September 2005
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	be appended to the selected Experiment.		be appended to the selected Experiment.
	After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.		After selecting an Experiment, there is a "Import from ArrayLIMS" link in the BasicMenu.
			[[Image:EMMAWiki$$WebDocumentation$$GeneralUsage$$ImportDatafromArrayLims$MainMenul.png]]
	Use this link to get to the main import page.		Use this link to get to the main import page.

imported>VirginieMittard at 13:14, 5 September 2005

2005-09-05T13:14:27Z

← Older revision		Revision as of 15:14, 5 September 2005
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	__NOTOC__		__NOTOC__
	= Import Data from ~~[[ArrayLims]]~~ =		= Import Data from 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]].

imported>VirginieMittard at 13:46, 25 August 2005

2005-08-25T13:46:16Z

← Older revision		Revision as of 15:46, 25 August 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. 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 ~~wich~~ color marker used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to ~~assigne~~ the correct [[Image and data upload\|images]] to the channels, just be careful not to switch channels if you don't want to. After the image to channel assignment you can ~~contiue~~ 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 ~~which takes some time because~~ the files are quite large.		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]] ==
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	== Step 5 Selection Overview ==		== Step 5 Selection Overview ==
	Finally choose a name for the selected arrays and take a look at the overview shown on this page		Finally choose a name for the selected arrays and take a look at the overview shown on this page
	to verify that all data are correct before you start the import.If you find a mistake in the selected data, please use your ~~browsers~~ 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.

	== 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 13:35, 25 August 2005

2005-08-25T13:35:36Z

← Older revision		Revision as of 15:35, 25 August 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. 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 wich color marker used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assigne the correct [[Image and data upload\|images]] to the channels, just be careful not to switch channels if you don't want to. After the image to channel assignment you can contiue 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 which takes some time because the files are quite large.		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 wich color marker used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assigne the correct [[Image and data upload\|images]] to the channels, just be careful not to switch channels if you don't want to. After the image to channel assignment you can contiue 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 which takes some time because 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.

	== Step 5 Selection Overview ==		== Step 5 Selection Overview ==

imported>VirginieMittard at 13:32, 25 August 2005

2005-08-25T13:32:31Z

imported>VirginieMittard at 13:29, 23 August 2005

2005-08-23T13:29:44Z

← Older revision		Revision as of 15:29, 23 August 2005
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	Use this link to get to the main import page.		Use this link to get to the main import page.

	The [[ArrayLims]] import is devided into 6 steps.		The ArrayLims import is devided into 6 steps.

	== Step 1 Select an ArrayLims Project ==		== Step 1 Select an ArrayLims Project ==

imported>VirginieMittard at 13:27, 23 August 2005

2005-08-23T13:27:25Z

← Older revision		Revision as of 15:27, 23 August 2005
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	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 remarkes. 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 remarkes. 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		== 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 wich color marker used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assigne the correct [[Image and data upload\|images]] to the channels, just be careful not to switch channels if you don't want to. After the image to channel assignment you can contiue 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 which takes some time because the files are quite large.		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 wich color marker used for which image (e.g. cy5 and cy3), and as long as you know what you did, you should be able to assigne the correct [[Image and data upload\|images]] to the channels, just be careful not to switch channels if you don't want to. After the image to channel assignment you can contiue 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 which takes some time because the files are quite large.

imported>VirginieMittard at 13:24, 23 August 2005

2005-08-23T13:24:47Z

← Older revision		Revision as of 15:24, 23 August 2005
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	To be able to import data to [[EMMAWiki\|EMMA]] one has to select an Experiment first. All imported Arrays will		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.		be appended to the selected Experiment.
	After selecting an Experiment, there is a "Import from [[ArrayLims]]" link in the [[BasicMenu]].		After selecting an Experiment, there is a "Import from ArrayLims" link in the BasicMenu.
	Use this link to get to the main import page.		Use this link to get to the main import page.

	The [[ArrayLims]] import is devided into 6 steps.		The [[ArrayLims]] import is devided into 6 steps.

	== Step 1 Select an [[ArrayLims]] Project ==		== 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.		Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLims]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLims]] Projects.
	Now have to select the one you want to import arrays from.		Now have to select the one you want to import arrays from.
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	== 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.

	== Step 5 Selection Overview ==		== Step 5 Selection Overview ==

imported>ThassoGriebel at 13:26, 18 April 2005

2005-04-18T13:26:26Z

← Older revision		Revision as of 15:26, 18 April 2005
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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 [[ViewResults]] page reachable from the [[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]].

← Older revision		Revision as of 15:32, 25 August 2005
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	= Import Data from [[ArrayLims]] =		= Import Data from [[ArrayLims]] =

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

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

	== Step 1 Select an ~~ArrayLims~~ Project ==		== 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.		Step one is the selection of an appropriate [[ArrayLIMSWiki\|ArrayLIMS]] Project. The selection box lists all accessible [[ArrayLIMSWiki\|ArrayLIMS]] Projects.
	Now have to select the one you want to import arrays from.		Now you have to select the one you want to import arrays from.

	== 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 ~~remarkes~~. 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.

	== Step 3 Image Selection ==		== Step 3 Image Selection ==