When running SCTransform, how to output the same gene count in scale.data same as in counts? #8580
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starislearning
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Hi
My function setting is: obj <- SCTransform(obj, assay = "RNA", do.correct.umi = TRUE,do.scale = TRUE, do.center = TRUE,method = "glmGamPoi", vars.to.regress = c("S.Score", "G2M.Score"), verbose = T,return.only.var.genes = FALSE). But even I set return.only.var.genes = FALSE. The gene count in scale.data is only 1/3 of gene count in counts, like:
What I want is the residuals for all genes in the SCTransform.
Thanks and kind regards,
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