Proper order of running FindSpatiallyVariableFeatures and PrepSCTFindMarkers #8480
pcantalupo
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Also, need to understand if I should use the original SCT data for FeaturePlots, VlnPlots, etc... or use the new SCT data generated by PrepSCTFindMarkers. |
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Hello
I have a merged Seurat object (Visium spatial data) from 4 individually SCTransformed Seurat objects. This is similar to how it is shown in the spatial vignette https://satijalab.org/seurat/articles/spatial_vignette#working-with-multiple-slices-in-seurat.
When I ran FindMarkers on my merged object, I got the message saying that PrepSCTFindMarkers needs to be run first. From the docs, this function is going to create a new count and data matrix in the SCT assay. I also want to determine spatially variable features with FindSpatiallyVariableFeatures however, I am not sure if I should use the new SCT data created by PrepSCTFindMarkers or run FindSpatiallyVariableFeatures before running PrepSCTFindMarkers.
What is the proper order of operations for these two functions? Thank you
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