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After specification of these types, the file will be validated to ensure that the values are valid for the types selected and that the file conforms to the requirements given above.

For more information, see Working with Annotations.

Annotation Field Configuration

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  • Annotation semantics: each annotation field (whether associated with a subject, image series, image or sample) must either:
    • be associated with an existing annotation definition known to the system,
    • be associated to an existing CDE in caDSR or
    • have sufficient semantic metadata recorded so that the field may be submitted for registration as a CDE in caDSR.
  • Field authorization: Each field must be either declared publicly visible or restricted to a list of groups. The default will be the visibility settings given at the study level. For more information, see Define Fields Page for Editing Annotations.
  • Whether the field is to be included in the results list for a given entity type (i.e. Subject, Sample, Image Series or Array Data) when browsing data.
  • Whether the field is to be included in simple single-input searches when browsing data.

For more information, see Adding Subject Annotation Data.

Sample Data Configuration

sample data, configuring for import;configuring:sample data for import;data import:configuring sample data forSample data may Sample data can be uploaded from either caArray 2 or from delimited-text import. Samples imported from caArray 2 may have annotation annotations updated by use of the delimited-text import functionality, if sample annotation is required. Import from caArray 2 requires specification of the following information:

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Next, the system indicates the available platforms and array data types available for the study samples. The Study Manager must indicate which platforms and data types to import and for each platform/data type combination must specify the following:

  • Whether to import the data
  • The visibility of the data; , either public or restricted to a set of groups. Low-level genotyping data (raw data and normalized) will always have has restricted visibility.

See also #Supplemental Files Configuration.

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  • Wiki Markup
    Affymetrix Expression Console – This software produces supplemental files. In Expression Console, use the "Export Result" function to create these files. Note that when you use an algorithm other than MAS5 to normalize the data (for example using RMA or Plier), Expression Console automatically creates a \[…{{summary.txt}}\] file that contains extra lines on top of the derived data results. The extra lines all start with a "#" to signify that it is a remark. These lines are ignored by caIntegrator parsing.
  • Agilent GeneSpring GX – This software can export a results table in .txt format.

Imaging Data Configuration

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  • NBIA grid server hostname (defaults to CBIIT instance)
  • NBIA grid server port (defaults to CBIIT instance port)
  • Protocol Id
  • Mapping of NBIA Patients to subjects imported from subject annotation data source. This may be specified by a comma-separated list in the format "subject identifier", "NBIA patient identifier" or by a regular-expression based mapping formula.
  • Which annotation fields to import from NBIA.

The system enables the Study Manager to navigate easily to the selected caArray 2 instance.

Additional annotation for either images or image series can be imported using the delimited-text import functionality.

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