Regarding copykat, it defines aneuploidy for the specified normal group

[mosy550]

Hello.
When I was running copykat, I specified a subgroup as normal cells. But why did the result of running it also define aneuploidy within this subgroup? Part of my code is as follows:

normal_cells <- rownames(msy@meta.data)[
msy@meta.data$Hep_res_0.3 == "Hep_5"
]
exp.rawdata <- as.matrix(msy@assays$RNA@counts)

copykat.test <- copykat(rawmat=exp.rawdata,
id.type="S",
ngene.chr=5,
win.size=25,
KS. The cut = 0.1,
sam.name="test",
distance="spearman",
norm.cell.names=normal_cells,
output.seg="FALSE",
plot.genes="TRUE",
genome="mm10",
n.cores=8)

May I ask if there is a problem with my code?
Thank you very much

[ChristineHOconnor]

Hi, I am also having the same issue. I ran CopyKAT on four single cell datasets and in all four samples, aneuploid cells were also called from the 'normal cells' group. In one sample, there were 12,044 cells and 10,593 were defined as normal (by cell type annotation). However, CopyKAT called 9,702 cells as aneuploid. If 'normal' cells can be aneuploid, how does defining a 'normal' cell subset help?