normalize_pos_controls: Positive control gene normalization

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

Positive control gene normalization

Description

Scale genes by the geometric mean of positive control genes. This step is conducted within processNanostringData, when normalization is set to "nCounter".

Usage

normalize_pos_controls(dat, logfile = "")

Arguments

dat	NanoString data, including expression matrix and gene dictionary.
logfile	Optional name of logfile to print messages, warnings or errors.

Value

NanoString data, with expression matrix now normalized by positive control gene expression.

Examples

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

dat <- read_merge_rcc(list.files(example_data, full.names = TRUE))

# Positive controls are identified in the RCC files, and used to 
# normalize the data
dat <- normalize_pos_controls(dat)

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