Normalize or transform expression values — normalize_expression • rsemflow

vst: DESeq2 size factors, then varianceStabilizingTransformation(blind = TRUE).
normalized-counts: counts divided by DESeq2 size factors (with the tximport average-length offsets).
log2-tpm: log2(TPM + 1).

Usage

normalize_expression(study, method = c("vst", "normalized-counts", "log2-tpm"))

Arguments

study: A rsemflow_study or study path.
method: One of vst, normalized-counts, or log2-tpm.

Value

A gene-by-sample numeric matrix.