In this step we import two different, but related, data tables:
- Plasma sample inventory: an Excel spreadsheet that describes different vials of plasma specimens.
- Assay result data: an Excel 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 Set - 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 Set - Plasma| Name | Sample Set | 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 Sets panel, click (Create New Sample Set).
- Provide the Name: "Plasma"
- You do not need to provide a Name Expression since the data already contains a unique identifier in a "Name" column.
- Note that the placeholder text shown in the box is not the default name expression, but an example of how one might look.
- You don't need to add a description or parent column import alias.
- Click Create.
- On the next screen, click Add Field to add each of the following fields:
Now you will see
Plasma included on the
Sample Sets 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.
- Specimen 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 Set) together.
- Experimental measurements - Columns M1, M2, M3.
| ParticipantId | SpecimenId | 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 General Assay Design and click Import.
- On the General Assay Import page:
- In the Name field, enter "Immune Scores"
- Set the Location to Current Folder (ELN).
- 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.
In the next step we will connect this data.
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