normalize_microarray: Normalize microarray data

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Normalize microarray data

Description

Normalize across samples to correct for technical variation using quantile normalization. Also log2-transforms the data.

Usage

normalize_microarray(
  exprs_mx,
  log2_transform = TRUE,
  force = FALSE,
  verbose = FALSE
)

Arguments

exprs_mx	matrix with background-corrected microarray expression data, one column per sample, one row per feature.
log2_transform	(boolean) Should log2 transform be performed before normalization? This should be FALSE for affy data which was read using RMA, which is already in log2 scale.
force	(boolean) Force log2 transform. If log2_transform is TRUE, this function will error if counts_dt does not have values greater than 100, unless force = TRUE.
verbose	print verbose logging statements?

Value

a matrix with one row per feature and one column per sample.

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.