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

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.

10x seurat scrnaseq
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updated by rpolicastro rpolicastro • written by simplitia • simplitia

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

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written by simplitia • simplitia

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

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written by rpolicastro rpolicastro

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?

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written by simplitia • simplitia

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

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written by rpolicastro rpolicastro

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