The microarray assay type allows you to collect run-level metadata from the user and combine it with metadata in the MageML file. For more information, see Microarray or complete the Microarray Assay Tutorial for a full walkthrough of the process.

Before you can import any microarray data, you must create an assay design, then browse to MageML files using the Data Pipeline. The Pipeline recognizes files with the .mage, MAGE-ML.xml, and _MAGEML.xml suffixes.

This page provides further details on default properties.

Assay Properties

  • Name. Required. Name of the assay design.
  • Description. Optional.
  • Channel Count XPath. Optional. XPath for the MageML that defines the number of channels for the microarray run. The server uses this value to determine how many samples it needs to get from the user. Defaults to:
/MAGE-ML/BioAssay_package/BioAssay_assnlist/MeasuredBioAssay/FeatureExtraction_assn/FeatureExtraction/
ProtocolApplications_assnlist/ProtocolApplication/SoftwareApplications_assnlist/SoftwareApplication/
ParameterValues_assnlist/ParameterValue[ParameterType_assnref/Parameter_ref/@identifier=
'Agilent.BRS:Parameter:Scan_NumChannels']/@value
  • Barcode XPath. Optional. XPath for the MageML that defines the barcode for the run. The server uses this value to match MageML files with associated samples. Defaults to:
/MAGE-ML/BioAssay_package/BioAssay_assnlist/MeasuredBioAssay/FeatureExtraction_assn/FeatureExtraction/
ProtocolApplications_assnlist/ProtocolApplication/SoftwareApplications_assnlist/SoftwareApplication/
ParameterValues_assnlist/ParameterValue[ParameterType_assnref/Parameter_ref/@identifier
='Agilent.BRS:Parameter:Scan_NumChannels']/@value
  • Barcode Field Names. Optional. The name of the field in a sample set that contains a barcode value that should be matched to the Barcode XPath's value. Multiple field names may be comma separated, and the server will use the first one that has a matching value.
  • Cy3 Sample Field Name. Optional. This is the name of the column whose cells contain Cy3 sample names. It is only used if you are using "Bulk Properties" (specifying the run properties in bulk). Defaults to: ProbeID_Cy3.
  • Cy5 Sample Field Name. Optional. This is the name of the column whose cells contain Cy5 sample names. It is only used if you are using "Bulk Properties" (specifying the run properties in bulk). Defaults to: ProbeID_Cy5.

XPaths

For Bulk, Run and Data Properties, you can include an XPath in the "Description" property for any field you include. This XPath will tell LabKey Server where to automatically find values for this field in the MAGEML file. Since this information is provided automatically, you are not prompted for the information while importing files. See the Microarray Assay Tutorial for examples of using XPaths.

Batch Properties

The user is prompted for batch properties once for each set of runs during import. The batch is a convenience to let users set properties once and import many runs using the same suite of properties. Typically, batch properties are properties that rarely change.

Properties included by default: None.

Run Properties

The user is prompted to enter run level properties for each imported file. These properties are used for all data records imported as part of a Run. This is the second step of the import process. You may enter an XPath expression in the description for the property. If you do, when importing a run the server will look in the MAGEML file for the value.

Properties included by default: None.

Data Properties

The user is prompted to select a MAGEML file that contains the data values. If the spot-level data within the file contains a column that matches the data column name here, it will be imported.

Properties included by default: None.

Finish Assay Design

After making changes, be sure to click Save or Save & Close at the bottom of the page.

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