normalize_housekeeping {NanoTube} | R Documentation

## Housekeeping gene normalization

### Description

Scale endogenous 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"))

[Package NanoTube version 1.0.0 Index]