normalize_random: Normalize data using random reference samples

In OVCARE/nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

Normalize data using random reference samples

Description

Normalize nanostring gene expression using randomly chosen samples for the reference-based approach for batch adjustment.

Usage

normalize_random(x, ref, n = 1, strata = NULL, seed = NULL)

Arguments

x	target data
ref	reference data
n	number of random reference samples to select for normalization
strata	a grouping variable for stratified random sampling. If strata has k levels, then n * k random samples are selected.
seed	random seed for reproducibility

Details

The number of randomly chosen numbers can be selected, and optionally a strata can be specified such that n reference samples are selected from each level (like a stratified bootstrap). In relation to the reference method, the random samples removed from ref form R1, the random samples removed from x form R2, and the remaining samples from x form Y. See refMethod() for details.

In subsequent analyses, we refer to a method using normalize_random(n) as the "Random n" method.

Value

normalized gene expression

Author(s)

Derek Chiu

OVCARE/nanostringr documentation built on Aug. 28, 2023, 1:26 p.m.