Tutorial - Connecting to caArray - Revision history

Smith at 21:46, 13 August 2008

2008-08-13T21:46:42Z

Smith at 21:15, 13 August 2008

2008-08-13T21:15:51Z

Smith at 21:15, 13 August 2008

2008-08-13T21:15:05Z

New page

=The Remote Open File dialog=
geWorkbench can retrieve data from certain remote data sources; currently only instances of the NCICB's caArray database are supported. The Open File dialog allows remote sources to be added to the list of those available either manually or through discovery using grid services. Entries (locations, parameters) for non-grid services can be edited.

Right-click on '''Project''' which will bring up the '''Open File''' dialog. Click the '''Remote''' radio button. The '''Open File''' dialog window will be expanded to include remote sources.

[[Image:T_OpenFile_Remote.png]]

They buttons at the bottom of the remote file dialog are:

'''Source''' button - lists remote resources.

'''Go''' button - downloads a list of all available experiments from the remote source.

'''Filtering''' - Allows one to see a list of particular types of experiements, such as by organism or chip type, on the remote source.

'''Add A New Resource''' button - Opens the Data Source Definition Page used to add a remote data source.

'''Edit''' button - Edits remote source parameters.

=Loading data from an instance of caArray=

==Setting up the connection==

You can '''Add a New Resource''' or '''Edit''' existing connection settings to set up a connection to an instance of caArray. The configuration for connecting to the production instance of caArray at the NCI is shown here:

[[Image:T_caArray_EditConnection.png]]

==Searching and viewing available experiments==

If you click on the red '''Go''' button next to the caArray data source at the bottom of the dialog, all available caArray experiments at that location will be displayed.

Instead, you can select only particular kinds of experiments by pushing the '''Filter''' button. Here we show experiments of type "Human" being selected.

[[Image:T_caArray_Filter.png]]

And here are the resulting entries in the database:

[[Image:T_caArray_Human_Expts.png]]

Select an experiment and push the '''Show Arrays''' button to see the individual array datasets available for download for this experiment.

[[Image:T_caArray_ShowArrays.png]]

==Downloading select array datasets==
Now we will select four of the arrays and push the '''Open''' button to begin the download. Dont' forget to click the '''Merge''' button first if desired to merge the data into a single dataset.

[[Image:T_caArray_Open4Arrays.png]]

You will be prompted to select the quantitation type from those available for the experiment. Here we select CHP Signal:

[[Image:T_caArray_QuantType.png]]

The resulting data set will appear in the Project Folders component:

[[Image:T_caArray_Loaded.png]]

← Older revision		Revision as of 21:46, 13 August 2008
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−	~~{{TutorialsTopNav}}~~

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−	~~=The Remote Open File dialog=~~
−	geWorkbench can retrieve data from certain remote data sources; currently only instances of the NCICB's caArray database are supported. The Open File dialog allows remote sources to be added to the list of those available either manually or through discovery using grid services. Entries (locations, parameters) for non-grid services can be edited.
−
−	~~Right-click on '''Project''' which will bring up the '''Open File''' dialog. Click the '''Remote''' radio button. The '''Open File''' dialog window will be expanded to include remote sources.~~
−
−
−	~~[[Image:T_OpenFile_Remote.png]]~~
−
−
−	~~They buttons at the bottom of the remote file dialog are:~~
−
−	~~'''Source''' button - lists remote resources.~~
−
−	~~'''Go''' button - downloads a list of all available experiments from the remote source.~~
−
−	~~'''Filtering''' - Allows one to see a list of particular types of experiements, such as by organism or chip type, on the remote source.~~
−
−	~~'''Add A New Resource''' button - Opens the Data Source Definition Page used to add a remote data source.~~
−
−	~~'''Edit''' button - Edits remote source parameters.~~
−
−
−
−	~~=Loading data from an instance of caArray=~~
−
−	~~==Setting up the connection==~~
−
−	You can '''Add a New Resource''' or '''Edit''' existing connection settings to set up a connection to an instance of caArray. The configuration for connecting to the production instance of caArray at the NCI is shown here:
−
−	~~[[Image:T_caArray_EditConnection.png]]~~
−
−
−	~~==Searching and viewing available experiments==~~
−
−	~~If you click on the red '''Go''' button next to the caArray data source at the bottom of the dialog, all available caArray experiments at that location will be displayed.~~
−
−	~~Instead, you can select only particular kinds of experiments by pushing the '''Filter''' button. Here we show experiments of type "Human" being selected.~~
−
−
−	~~[[Image:T_caArray_Filter.png]]~~
−
−
−
−	~~And here are the resulting entries in the database:~~
−
−	~~[[Image:T_caArray_Human_Expts.png]]~~
−
−
−
−	~~Select an experiment and push the '''Show Arrays''' button to see the individual array datasets available for download for this experiment.~~
−
−	~~[[Image:T_caArray_ShowArrays.png]]~~
−
−
−	~~==Downloading select array datasets==~~
−	~~Now we will select four of the arrays and push the '''Open''' button to begin the download. Dont' forget to click the '''Merge''' button first if desired to merge the data into a single dataset.~~
−
−	~~[[Image:T_caArray_Open4Arrays.png]]~~
−
−
−
−	~~You will be prompted to select the quantitation type from those available for the experiment. Here we select CHP Signal:~~
−
−	~~[[Image:T_caArray_QuantType.png]]~~
−
−
−
−	~~The resulting data set will appear in the Project Folders component:~~
−
−	~~[[Image:T_caArray_Loaded.png]]~~

← Older revision	Revision as of 21:15, 13 August 2008
Line 1:	Line 1:
−	+	{{TutorialsTopNav}}
−