What are the units for the sctransform SCT scale.data slots?

Question

[simplitia]

Hi using the Seurat here; when using the sctransform to normalize, what is the unit in the count data matrix?

pbmc[["SCT"]]@scale.data

I'm assuming its non-log TPM? but wanted to make sure.

thanks.

[rpolicastro]

Those are the pearson residuals from the regression model. See the original publication and the SCTransform v2 publication for more information.

[simplitia]

thanks you are correct. Do you know how to extract TPM counts?

[rpolicastro]

How did you quantify your scRNA-seq? Most software returns UMI counts, not TPMs.

[simplitia]

sorry I'm not asking the questions correctly here. For downstream comparisons, say I want to compare group B to group C visually. Which of the data slots would be best to use? So scale.data slots are the Pearson Residuals (as per the publication); counts slots are from the Negative Binomial model to median transcript count per cell and the data are log2 transformed of counts. can I just take the log2 of the scale.data and plot the two groups?

[rpolicastro]

For visualization use the data or scale.data slots in the RNA assay after running NormalizeData and ScaleData.