Plan Analysis
The Planned Analyses tab allows you to view and manage planned analyses that are configured to auto-launch when sample data becomes available. This is useful when you want to set up an analysis before your samples have been scanned.
To access this tab, navigate to the Microarray Hub and select Planned Analyses.
If your sample data is already available and you want to start an analysis immediately, see Launch Analysis.
Planning an Analysis
Planning an analysis allows you to configure an analysis before your sample data has been scanned and uploaded. Once configured, the planned analysis will automatically launch when all sample data becomes available.
Select Plan an analysis from the Planned Analyses tab to create a new planned analysis. Use the following steps to configure a planned analysis:
Enter the Analysis Name
Use the Select Project link to choose the project for your output files To select an existing project, click the radio button next to the desired project name. You can also create a project by clicking the New button in the project selection window.
Select the Type of Analysis Further detail of each Type of Analysis is available in DRAGEN Array Applications and Polygenic Risk Score Software
(Optional) Create a custom configuration via the "Add Custom Configuration" option in Configuration Settings. Custom configurations must be assigned a name and product files can be uploaded or selected. Details on file name constraints can be found in the ICA documentation. Custom configuration options vary by Type of Analysis selected. More details are available in section DRAGEN Array Applications.
Select your preferred option in the Configuration Settings drop-down menu Configuration setup will vary based on the Type of Analysis selected. More details are available in section DRAGEN Array Applications.
Select Next
Select Import Sample Sheet to upload a sample sheet Download a template sample sheet by selecting the Download Template link. The samples listed in the sample sheet do not need to be scanned or have data uploaded yet. More details are available in the Sample Sheet section.
Specify the Maximum failed scanned samples threshold This setting determines how many samples can fail during scanning before the planned analysis is aborted.
A sample is considered failed during scanning when the stripe registration is less than 0.75. Failed stripes are flagged as potentially misregistered and appear colored red in the Scan Progress Indicator window of the iScan Control Software.
Save the planned analysis
How Planned Analyses Execute
Once a planned analysis is saved, the system monitors for sample data availability:
Auto-launch: When all sample data listed in the sample sheet becomes available, the analysis will automatically launch.
Abort on threshold exceeded: If the number of samples that failed during scanning exceeds the Maximum failed scanned samples threshold, the planned analysis will be aborted.
Launch with passing samples: If some samples fail but the count is within the threshold, the analysis will launch automatically with only the passing samples.
Viewing Planned Analyses
The Planned Analyses tab displays a list of all planned analyses. Click on any analysis to view its details, including the configuration settings and sample information.
Overview Card
The overview card at the top of the Planned Analyses tab provides a quick summary of your analyses by status:
Planned: Total number of analyses with planned status (not yet launched)
Planned & Launched: Number of analyses that have been planned and subsequently launched
Aborted Before Launch: Number of analyses that were aborted before launching
You can filter the analyses table by selecting a date range in the overview card. This will display only the planned analyses that have been modified within the selected date range. Clicking on any of the status count numbers will automatically filter the analyses table to show only analyses with that status.
Viewing Single Analysis Details
Click on any planned analysis in the table to view its complete details. The details page is organized into three sections:
Configuration
The Configuration section displays the core settings for your planned analysis:
Analysis Name: The name you assigned to the planned analysis
Project: The project where the analysis output files will be stored
Analysis Type: The type of analysis selected
Detailed Configuration Settings: The specific configuration parameters for your selected analysis type
Samples
The Samples section contains information about the samples included in your planned analysis:
Samplesheet: Download the samplesheet that was imported for this analysis
Maximum Failed Samples Allowed: The threshold you set for how many samples can fail during scanning before the planned analysis is aborted
Status
The Status section shows the current state and progress of your planned analysis:
Status: The current status of the analysis (e.g., planned, launched, aborted)
Array Status Summary: A summary of the scanning status for all samples in the analysis or the launch status
Export Sample Status: Download a detailed file containing the status of every individual sample in the analysis. This file provides information about each sample's processing status and any errors encountered.
Sample Statuses and Reasons
When you export the sample status, each sample will have a Status and a Reason. There may be multiple possible reasons for each status, depending on the sample's situation. The reason provides additional explanation for why the sample received its status.
Ready
Sample will be included in analysis due to successful data upload.
The sample data is available and meets all requirements for inclusion in the analysis.
Failed
Sample will be excluded from analysis due to scanning failure.
Sample failed during scanning because the stripe registration is less than 0.75 (flagged as potentially misregistered in iScan Control Software).
Pending
Sample is pending data upload.
The sample is not ready for analysis because it has not yet been scanned or its data has not been uploaded.
Deleting Planned Analyses
Only planned analyses with a planned status (analyses that have not yet launched) can be deleted from this page. Deleting a planned analysis removes it from the system and prevents it from auto-launching when sample data becomes available.
To delete planned analyses:
Check boxes for individual analyses on the left-hand side, or
Use the top checkbox to select all analyses on the current page for bulk deletion.
Deleting a planned analysis will permanently remove it and the action cannot be undone. Analyses that have already launched cannot be deleted from this page.
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