normalize_housekeeping: Housekeeping gene normalization

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

Housekeeping gene normalization

Description

Scale endogenous and housekeeping genes by the geometric mean of housekeeping genes. This should be conducted after positive control normalization and background correction. This step is conducted within processNanostringData, when normalization is set to "nCounter".

Usage

normalize_housekeeping(dat, genes = NULL, logfile = "")

Arguments

dat	NanoString data, including expression matrix and gene dictionary.
genes	List of housekeeping genes to use for normalization. If NULL (default), will use all genes marked as "Housekeeping" in codeset.
logfile	Optional name of logfile to print messages, warnings or errors.

Value

NanoString data, with expression matrix now normalized by housekeeping gene expression.

Examples

example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube")

# Load data, positive control normalization, and background filtering
dat <- read_merge_rcc(list.files(example_data, full.names = TRUE))
dat <- normalize_pos_controls(dat)
dat <- remove_background(dat, mode = "t.test", pval = 0.05)

# Normalize by genes marked "Housekeeping" in RCC files
dat <- normalize_housekeeping(dat)

# Normalize by specified housekeeping genes (gene symbol or accession)
dat <- normalize_housekeeping(dat,
                       genes = c("TUBB", "TBP", "POLR2A", "GUSB", "SDHA"))

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.