DE with unintegrated data #4645
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planti-body
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I am performing differential gene expression analysis on a (treatment/control) dataset that has not been integrated, only SCTransformed.
In this case, do I still need to revert to the "RNA" assay and run "NormalizeData" before performing FindAllMarkers, FindMarkers, and FindConservedMarkers? Or can I remain on the "SCT" assay?
I've only been encountering this question in terms of integrated data, so I'm confused about my scenario
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