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Note that you can continue to work in caIntegrator while the study is being deployed.

Managing a Study

Once you have started to create a study or have deployed it, you can view metadata for the study on the Manage Studies page. For example, the metadata reveals the deployment start and finish dates and times, and whether or not caArray genomic data imported into the study has been updated since deployment. (caIntegrator refreshes caArray data hourly.) If you see that the caArray data has been updated, you could go to the study itself and ascertain the changes. You may decide to keep it as it is or redeploy the study.

Additionally, on this page you can update the study in the following ways:

• Add new attributes (annotations) and upload relevant data to the existing study.
• Disable or re-enable a study
• Delete the study
• Modify existing annotation definitions
• Reload a subset of a study data and re-deploy the study and perform new analyses
• Re-deploy the entire study with new set of data and mappings.

Editing or Updating a Study

To update, edit or delete a study, follow these steps:

1. On the left sidebar, click Manage Studies. The Manage Studies page appears, shown in the following figure.
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   All of the "in process" or "completed" studies display on this page with associated metadata. Note that whoever edited or updated the study last is shown in the Last Modified Column, indicated as the Study Manager.
2. Click the Edit link corresponding to your study of choice to open the Edit Studies page, shown in the following figure.
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   On this page you can edit any details such as adding or deleting files, survival values, and so forth. For information about working with the Edit Study feature, see #Creating/Editing a Study.
3. Click the Delete link to delete the corresponding study.

Disabling or Re-enabling a Study

Only the study manager of a study can disable or re-enable a study. To perform either of these tasks, follow these steps:

1. On the left sidebar, click Manage Studies. The Manage Studies page appears, displaying the studies for which you have permissions.
2. In the Action column, click the Disable link corresponding to your study of choice.
3. To re-enable a study, click the Enable link corresponding to the selected study.

The Manage Studies page refreshes after clicking either of these links. The page now shows that the changed status of the study.

• Disabling a study is recorded in the study log.
• A disabled study is not searchable nor available to any user.
• A disabled study cannot be edited nor copied.
• When a study is re-enabled, there is no data change to the study from the original.
• A disabled study being re-enabled must not duplicate the name of a currently enabled study.

Managing Platforms

caIntegrator supports a limited number of array platforms, all of which originate from Agilent or Affymetrix. While they do not represent all of the platforms supported by caArray, caIntegrator must have array definitions loaded for the platforms it supports, and be able to properly load the data from caArray and parse it. For more information, see B - Platforms Supported by caIntegrator.

You can create a study without genomic data, but you cannot add genomic data to a caIntegrator study without a corresponding supported array platform. If you add more than one set of genomic data to the study, you can specify more than one platform for the study.

On the Manage Platforms page, you can identify, add or remove supported platforms.

To manage platforms in caIntegrator, follow these steps:

1. Click Manage Platforms on the left sidebar.
   The Manage Platforms page that opens lists in the Existing Platforms section the platforms caIntegrator currently supports, those that the system can pull from caArray. See the following figure. You can also add a new platform by entering information in the fields in the Create a New Platform section.
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2. To add a platform, in the Platform Type field, select the appropriate platform type from the drop down list.
3. Click Browse to navigate for the Affymetrix or Agilent file you want to add.

   Info
   title Note
   Tab-delimited .txt or .tsv Agilent platform annotation files must contain the following column headers: ProbeId, GeneSymbol, GeneName and Accessions.

4. Enter a Platform Name if the file is a NON-GEML.xml file.
   Depending on the Platform Type you select, there may be other parameters to provide here as well, such as Platform Channel Type for an Agilent platform.
5. Click the Browse button to browse for the appropriate annotation file.
6. When you have located it, click Open in the Upload File dialog box. The system displays the annotation file you select in the Annotation File box.
7. Once all parameters have been entered, click Create Platform.

The platform deployment can be time-consuming. If the platform takes more than 12 hours to deploy, caIntegrator displays a "timed out" message. At that point, you can delete the platform, even if it has not loaded to the system.