Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
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12 weeks ago
Adrian • 0


I've got a seurat object of 2 samples integrated after QC and SCTv2. I then performed clustering and PrepSCTfindMarker followed by findMarker. These all went smoothly. Then I made a subset from 3 clusters, performed clustering on the subset and proceed to find marker.

From the SCTv2 vignette, it states that if the original object before subsetting has performed PrepSCTfindMarker, the subsetted object can run findMarker directly with recorrect_umi = FALSE. However, i get the following error asking me to run PrepSCTFindMarkers again, wouldn't that normalize a second time?: Error in FindMarkers.SCTAssay(object = data.use, slot = slot, cells.1 = cells$cells.1, : Object contains multiple models with unequal library sizes. Run PrepSCTFindMarkers() before running FindMarkers().

Thanks in advance!

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