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- Click the Normalized counts node
- Click Exploratory analysis in the task menu
- Click PCA
You can choose Features contribute equally to standardize the genes prior to PCA or allow more variable genes to have a larger effect on the PCA by choosing by variance. By default, we take variance into account and focus on the most variable genes.
If you have multiple samples, you can choose to run PCA for each sample individually or for all samples together using the Split cells by sample option.
- Click Configure to access the advanced settings
- Click Output Generate PC Quality Measures quality measures
- Click Apply
- Click Finish to run
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