Closed mckoch234 closed 10 months ago
mass-a
commented
1 year ago Hello! can you tell us if you are using objects in Seurat v5 format? it would be great if you could provide a piece of code and your SessionInfo(), so that we can try to reproduce your error. In general, regardless of how you merged/integrated your dataset, I would recommend to provide uncorrected data ('RNA assay') to ProjecTILs, possibly split by sample (see this case study for an example.
-m
alicekao1118
commented
7 months ago @mckoch234 could you share how you fix this issue? I got the same error. But Seurat v5 can't JoinLayers()with SCT assays.
mckoch234
commented
7 months ago I used PrepSCTFindmarkers().
On Wed, Mar 27, 2024 at 11:14 PM alicekao1118 @.***> wrote:
@mckoch234 https://github.com/mckoch234 could you share how you fix this issue? I got the same error. But Seurat v5 can't JoinLayers() with SCT assays.
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Hello, I am trying to run run.projectiles with the sct assay however I am getting this error Error: SCT assay is comprised of multiple SCT models. To change the variable features, please set manually with VariableFeatures<- . I did set it manually with variable featuers however it is still giving me the same error.