This topic explains how to automatically infer an assay design based on your spreadsheet data.
Assay Designs and Assay Types
An assay
design defines the basic shape of your data, including:
- the column names
- the column datatypes (integer, text, etc.)
- the contextual data (also known as "metadata") about your assay, such as who ran the assay, on what machine, and for which client/project.
To create an assay design, you customize an assay
type. Each assay type is associated with a particular class of assay instrument or diagnostic test. For example, there are assay types for ELISpot, Luminex, and others, each intended to fit the data requirements of the particular assay workflow. There is also a "General" assay type that you can customize to fit
any sort of assay data.
Note that developers can create their own assay types; administrators can create their own assay designs based on the available types.
In the step we will customize this "General" assay type to create our design. In particular, we will ask LabKey Server to examine our data spreadsheets and automatically infer an assay design to fit the data.
Create a New Assay Design by Inference
- In the Files web part, locate and select the file LabKeyDemoFiles/StudyDemoFiles/Assays/Generic/GenericAssay_Run1.xls.
- Click Import Data.
- Select Create New General Assay Design and click Import.
- You are taken to the General Assay Import page.
Note that LabKey Server has examined the file and
inferred a "best guess" assay design for you.
- On the General Assay Import page, in the Name field, enter "GenericAssay".
- Uncheck column5 and column6.
- Click Show Assay Designer.
Modify the Assay Design
The basics of the assay design (the field names and data types) have been decided upon. We are now ready to finish up the design process using the full Assay Designer. We will add some metadata fields to help us track the machine's operator and settings.
Batch Fields. During assay data import, an operator will be prompted once for these fields for each set of data files.
- In the section GenericAssay Batch Fields:
- Click Add Field, enter the Name "OperatorEmail", and enter the Description: "The person who ran the diagnostic test."
- Click Add Field, enter the Name "Machine", and enter the Description: "The diagnostic test machine".
Run Fields. During assay data import, an operator will be prompted to enter run-level properties for each file they import.
- In the section GenericAssay Run Fields:
- Click Add Field, enter the Name "MachineSetting", set the Type to Integer, and enter the Description "The configuration settings on the assay machine."
- Scroll down to the bottom of the page and click Save & Close.
Now the assay design is complete and we are ready to import assay data files into our assay design.
Complete the Data Import
You may have forgotten by now that we are in the middle of importing a spreadsheet data file! It's now time to complete the import process.
- On the Data Import: Batch Properties page:
- Enter a fictional or non-fictional email address for Operator Email. (Notice that this is a custom field you just added to the assay design.)
- Enter some value for Machine. (This also is a custom field you added to the assay design.)
- Click Next.
- On the Data Import: Run Properties and Data File page:
- Enter some integer value for Machine Setting. (Another custom field you added to the design.)
- Click Save and Finish. (Note the data file you are about to import: GenericAssay_Run1.xls)
You are taken to the
GenericAssay Runs page. This page shows you which data files have been imported using the assay GenericAssay design.
Next…
Import Assay Data
