normalize_pools: Normalize data using common pools
In OVCARE/nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

View source: R/normalize_pools.R

normalize_pools

R Documentation

Normalize data using common pools

Description

Normalize nanostring gene expression using common pools between two CodeSets.

Usage

normalize_pools(
  x,
  x_pools,
  ref_pools,
  p = 3,
  weigh = TRUE,
  same_codeset = FALSE
)

Arguments

`x`	target data
`x_pools`	target pool samples
`ref_pools`	reference pool samples
`p`	number of pool sample sets. Defaults to 3.
`weigh`	logical; if `TRUE`, the average expression in `x_pools` is reweighed by the distribution of the `p` pool sample sets in `ref_pools`.
`same_codeset`	logical; if `TRUE`, the target pool samples are collected from the same codset as the reference pool samples. This means the pool numbers from the file names use an older format where two-digit pools still pertain to pools 1, 2, or 3.

Details

The target and reference expression samples, as well the target and reference pool samples all need to be specified. We recommend reweighing the target pool samples when calculating the average expression by the distribution of reference pools.