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On the Edit Study page where you have selected and added the subject annotation data, click the Add New button under Genomic Data Sources. You can upload genomic data only from caArray.
This opens the Edit Genomic Data Source dialog box. Enter the appropriate information in the fields, shown in the following figure and described below.
|| Field Types || Field Description ||Field
Description
caArray Web URL
Enter the URL for the caArray instance to be used for the genomic data sources. This will enable a user to link to the referenced caArray experiment from the study summary page.
caArray Host Name
Enter the hostname for your local installation or for the CBIIT installation of caArray. If you misspell it, you will receive an error message.
caArray JNDI Port
Enter the appropriate server port. See your administrator for more information. Example: For the CBIIT installation of caArray, enter 8080 .
caArray Username and caArray Password
If the data is private, you must enter your caArray account user name and password; you must have permissions in caArray for the experiment. If the data is public, you can leave these fields blank.
caArray Experiment ID
Enter the caArray Experiment ID which you know corresponds with the subject annotation data you uploaded. Example: Public experiment "beer-00196" on the CBIIT installation of caArray (array.nci.nih.gov). If you misspell your entry, you will receive an error message.
Vendor
Select either Agilent or Affymetrix.
Data Type
Select Expression or Copy Number.
Platform
If appropriate, select the Agilent or Affymetrix platform.
Info title Multiple platforms Because you can add more than one set of genomic data to a study, a study can also have multiple platforms, one for each set of genomic data.
Central Tendency for Technical Replicates
If more than one hybridization is found for the reporter, the hybridizations will be represented by this method.
Indicate if technical replicates have high statistical variability
If more than one hybridization is found, checking this box will display a ** in the genomic search results when a reporter value has high statistical variability.
Standard Deviation Type
When the checkbox for indicating if technical replicates have high statistical variability is checked, this parameter becomes available. Select in the drop-down the calculation to be used to determine whether or not to display a ** (see previous bullet point).
--Relative calculates the Relative Standard Deviation in percentage value
--Normal calculates the Standard Deviation in numeric valueStandard Deviation Threshold
When the checkbox for indicating if technical replicates have high statistical variability is checked, this parameter becomes available. This is the threshold at which the Standard Deviation Type is exceeded and the reporter is marked with a **.
- Click Save.
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On the Edit Study page under the Imaging Data Sources section, click the Add Newbutton.
Info title Imaging data source If you have already provided an imaging data source, it is listed in this section of the Edit Study page. To edit the imaging data source, click the Edit button which opens the same dialog box described in the following steps.
In the Edit Imaging Data Source dialog box, configure the appropriate imaging data source information in the fields as shown in the selected area of the following figure and described below. Fields with an asterisk are required.
|| Fields || Description ||Field
Description
NBIA Server Grid URL*
Enter the URL for the grid connection to NBIA.
NBIA Web URL
Enter the URL of the web interface of the NBIA installation.
NBIA Username and NBIA Password
This information is not required, as currently all data in the NBIA grid is Public data.
Collection Name
Enter the name/source for the collection you want to retrieve.
Current Mapping
If a mapping file has already been uploaded to the study to map imaging data, the file name displays here.
Select Mapping File Type
Click to select the file type:
--Auto – No file is required. Selecting this takes all subject annotation subject IDs and attempts to map them to the corresponding ID in the collection in NBIA. If the ID does not exist in NBIA, then no mapping is made for that ID.
--By Subject – Requires a mapping file to be uploaded. The "subject annotation to imaging mapping file" must be in CSV format with two columns that map the caIntegrator subject annotation subject ID to the NBIA subject ID.
--By Image Series – Requires a file to be uploaded. The subject annotation to imaging mapping file needs to be a two column mapping (CSV) from the caIntegrator subject annotation subject ID to the NBIA study instance UID.Subject to Imaging Mapping File
Click Browse to navigate to the appropriate subject annotation to imaging mapping file. See the Select Mapping File Type* field description.
Info title Mapping files uploaded? If mapping files have already been uploaded for the data sources you are editing, the Image Mapping tables of the dialog box show the mapping from NBIA Image Series Identifier to caIntegrator Subject Identifier.
- Click Save to upload the data from NBIA to caIntegrator. The imaging data displays on the Edit Study page under the Imaging Data Sources section, as shown in the following figure.
- Once the data is uploaded, you can add image annotations. For more information, see Adding or Editing Image Annotations.
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