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Obtain and add files to the project
Follow along to add files to your Xenium project: Add files to the project.
Perform quality analysis / quality control and filtering
- Filter the data including control probes using the Filter features task
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- task
- Choose Feature metadata filter
- Include the Gene Expression features
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- Click Finish
- This results in a Filter features task (rectangle) and node (circle) results.
- Right click the circle to Rename data node to "Filtered to only gene expression".
- Click the circular "Filtered to only gene expression" results node and select the Single cell QA/QC task from the context sensitive menu on the right.
- When the task completes it will be opaque and no longer transparent with a progress bar.
This task does not produce a circular results node but instead a rectangle.
Double click the opaque rectangle task to open and filter cells as described here. Apply the observation filter to the "Filtered to only gene expression" results node. This results in a "Filtered cells node".
Normalize the data
- Select the "Filtered cells node" and choose the Normalization task from the Normalization and scaling drop-down in the task menu
- Click the Use recommended button to proceed with these settings
- Click Finish
This results in a Normalized counts node as shown below in the pipeline.
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