In this step we import two different, but related, data tables to the
Lab Workflow tutorial folder you just created:
- Plasma sample inventory: a spreadsheet that describes different vials of plasma.
- Assay result data: a spreadsheet that holds the experimental results of assaying the plasma.
These tables are connected by the fact that the assay data
describes properties of the plasma in the vials. We will capture this relationship in the next step when we link these two tables together using a LabKey Server device called a
lookup. In the current step, we will simply import these tables to the server.
Add Sample Type - Plasma
We will import information about the individual sample vials, such as the tissues stored and the barcode of each vial, like the table shown below.
Sample Type - Plasma
| Name | Sample Type | Flag | Status | LocationId |
|---|
| vl-100 | Plasma | | Received | i-123456 |
| vl-200 | Plasma | Flagged for review | Results Invalid | i-123457 |
| vl-300 | Plasma | | Job Assigned | i-123458 |
| vl-400 | Plasma | | In Transit | i-123459 |
| vl-500 | Plasma | | Contaminated | i-123460 |
| vl-600 | Plasma | | Preserved | i-123461 |
| vl-700 | Plasma | | Results Verified | i-123462 |
- Download the sample file Plasma.xlsx from this page.
- Click the Vials tab.
- On the Sample Types panel, click New Sample Type.
- Provide the Name: "Plasma"
- You do not need to provide a Naming Pattern since the data already contains a unique identifier in a "Name" column.
- You don't need to add a description or parent column import alias.
- Click the Fields panel to open it.
- Click Manually Define Fields.
- Click Add Field to add each of the following fields:
Now you will see
Plasma included on the
Sample Type web part.
- Click Plasma to open it.
- Click Import More Samples.
- Click Upload file (.xslx, .xls, .csv, .txt) to open the file upload panel.
- Leave the Import Options box for "update" unchecked.
- Click Browse and select the Plasma.xlsx file you just downloaded.
Import Assay Data - Immune Scores
Next, we import the data generated by assays performed on these plasma vials. The data includes:
- Participant IDs - The subjects from which the samples were drawn.
- Sample IDs - Note these values match the Name column in the Plasma table. This fact makes it possible to link these two tables (Assay and Sample Type) together.
- Experimental measurements - Columns M1, M2, M3.
| ParticipantId | SampleId | Date | M1 | M2 | M3 |
|---|
| pt-1 | vl-100 | 4/4/2020 | 1 | 0.8 | 0.12 |
| pt-1 | vl-200 | 6/4/2020 | 0.9 | 0.6 | 0.22 |
| pt-1 | vl-300 | 8/4/2020 | 0.8 | 0.7 | 0.32 |
| pt-2 | vl-400 | 4/4/2020 | 0.77 | 0.4 | 0.33 |
| pt-2 | vl-500 | 6/4/2020 | 0.99 | 0.5 | 0.44 |
| pt-2 | vl-600 | 8/4/2020 | 0.98 | 0.55 | 0.41 |
| pt-3 | vl-700 | 4/4/2020 | 0.94 | 0.3 | 0.32 |
| pt-3 | vl-800 | 6/4/2020 | 0.8 | 0.77 | 0.21 |
Follow the instructions below to import the assay data into the server.
- Download the file immune-score.xlsx from this page. This is the data-bearing file. It holds the data results of your experiment, that is, the values measured by the instrument.
- Click the Experiments tab.
- Drag-and-drop this file into the Files panel.
- In the Files panel select the file immune-score.xlsx and click Import Data.
- In the Import Data pop-up dialog, select Create New Standard Assay Design and click Import.
- On the Assay Import page:
- In the Name field, enter "Immune Scores"
- Set the Location to Current Folder (Lab Workflow).
- Click Begin Import.
- On the Data Import: Batch Properties page, do not change any values and click Next.
- On the Data Import: Run Properties and Data File page, do not change any values and click Save and Finish.
- Click the Assay Results tab.
- You will now see the Immune Scores assay that you just defined.
In the next step we will connect this data.
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