adityamahadevaniyer
commented
1 year ago seu = seurat.object
sample.groups = seu$group
cell.groups = seu$celltype
sample.per.cell = seu$orig.ident
ref.level = “Untreated”
target.level = “Treated”
cao <- Cacoa$new(seu, sample.groups=sample.groups, cell.groups=cell.groups, sample.per.cell=sample.per.cell, ref.level=ref.level, target.level=target.level, graph.name= “SNN1”) I did create a graph name while running FindNeighbors()
The cao object is successfully created but i am unable to run these commands
cao$estimateCellLoadings()
Error- dimensions should to be positive
cao$estimateExpressionShiftMagnitudes()
Error- 2 factor level is needed
Hi team, I have been using Seurat object for the analysis. Could you please get clarify what do you mean by sample.per.cell argument? I have been inputting two factor group information under sample.groups and annotated cell type column as cell.groups. if I use orig.ident column as sample.groups., I get an error saying sample groups must be a two level factor describing which samples are being contrasted. Thank you, Aditya