normalize_pos_controls {NanoTube} | R Documentation

## 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)

[Package NanoTube version 1.0.0 Index]