Seurat: Discrete expression values after SCTransform

[lc822]

Hi,

If I plot a violin plot on the "data" slot after running SCTransform, the expression values seem to take only specific values (see plot below). Is this what I should be seeing?

Many thanks,
Lucy

[yuhanH]

SCTransform will store the normalized gene value in the scale.data slot.
You could choose scale.data slot in the violin plot.

[baracus37]

Hi, I am having the same issue after running SCTransform. And its does not matter which slot is used for plotting. Interestingly, looking at the SCTransform vignette the Violin Plots shown there towards the end of the page show the same phenomenon. I would be really interested in an explanation for this!