The assay progress report is designed to capture the specimen collection and assay processing lifecycle in a study. It displays the current status of which specimens have been collected and processed in your study. For each assay in your study, the report displays some status value for each participant/timepoint:
- whether the specimen has been collected or not
- whether assay results are available or not, and
- whether any adverse events have occurred, such as unusable or unexpected assay results
For example the status report below shows that most specimens have been successfully processed resulting in valid assay data, but one participant (PT-102) has an incomplete specimen processing history.
Assay progress reports are only available in a study folder. The following data sources are used to render the assay progress report:
|Data Source||Required?||Description||Source Schema and Table(s)|
|Participants||Required||The study must have participant data present.||study.Participant|
|Visits||Required||Study visits must be defined. Both date-based or visit-based studies are supported.||study.Visit|
|Assay Schedule||Required||Assay schedules must be defined, as described in the topic Manage Assay Schedule.||study.AssaySpecimen |
|Assay results||Required||Some table must be present to hold assay results. This can be a dataset or an assay design that has been copied to the study.||User defined assay results.|
|Specimen status query||Optional (see below for details)||Specimen status information is drawn from a query. Any query, such as a query based on a list, can serve this function as long as it has the required fields.||User defined query.|
The Specimen status query must expose the following fields:
- ParticipantId (of type String)
- VisitId (of type Integer)
- SequenceNum (of type Double)
- Status (of type String)
Allowed values for the Status field are list below. Allowed values are case-sensitive.
Note that the Specimen status query
is not strictly necessary to render a report. If the query is omitted, a simple report can be rendered based on the assay results in the study: if assay results are present for a given Participant/Visit, then the report will display the status "available" (
); otherwise "expected" (
) will be displayed, as shown below.
Create the Assay Progress Report
Once the data sources are in place, you can add a progress report for any of your assays.
- Click the Clinical and Assay Data tab.
- On the Data Views web part, click the drowndown triangle () and select Add Report > Assay Progress Report
- On the Create Assay Progress Repoort screen, for each assay you wish to include in the report, click the pencil icon ().
- This brings up Status Information Query pop up dialog. Use the dropdowns to point to the query which contains the specimen status information and click Submit. (Note if no status query is selected, then the Specimen Repository will be used to display a simplified report by default, see above for details.)
- The make the report visible to Readers or above, select the checkmark Share this report with all users?. Leaving this checkmark unselected makes it visible only to you and other Administrators.
- To finish the progress report, click Save
- The progress report is added to the Data View web part. To view the report click it in the Data Views web part, or add it to a study tab using the Report web part.
Export to Excel
The Export to Excel
button is activated when a single assay is selected for display. Clicking Export downloads all of the assay data for the selected assay.