tmm: Trimmed Mean of M-Values (TMM) Normalization
In roryk/bcbioRnaseq: RNA-Seq Utilities

Description Usage Arguments Value Author(s) See Also Examples

TMM normalization is recommended for RNA-seq data generally when the majority of genes are not differentially expressed. We use this as a quality control tool when plotting counts per gene.

tmm(object)

## S4 method for signature 'bcbioRNASeq'
tmm(object)

## S4 method for signature 'DESeqDataSet'
tmm(object)

## S4 method for signature 'matrix'
tmm(object)

object

Object.

matrix.

Michael Steinbaugh

Other Data Functions: counts, metrics, tpm

# bcbioRNASeq ====
tmm(bcb_small) %>% summary()

# DESeqDataSet ====
tmm(dds_small) %>% summary()

# matrix ====
counts(bcb_small) %>% tmm() %>% summary()