array_normaliseSE2: Normalise microarray data using lumiN function

In kauralasoo/eQTLUtils:

Normalise microarray data using lumiN function

Description

Normalise microarray data using lumiN function

Usage

array_normaliseSE2(
  se,
  norm_method = "quantile",
  assay_name = "exprs",
  log_transform = TRUE,
  adjust_batch = FALSE
)

Arguments

se	SummarizedExperiment file to be normalised
norm_method	Normalisation method from quantile, rsn, ssn, loess, vsn, rankinvariant (Default:quantile)
assay_name	Assay name to be normalised (exprs or batch_exprs)
log_transform	Boolean value if intensities should be log2 transformed (Default:TRUE)
adjust_batch	Boolean value if data should be adjusted for batch effects before normalisation (Default:FALSE)

Value

SummarizedExperiment with assay 'norm_exprs'

Author(s)

Liis Kolberg

kauralasoo/eQTLUtils documentation built on March 12, 2023, 8:50 p.m.