HKnorm {nanostringr}

Normalization to Housekeeping Genes

Description

Normalizes the gene expression of NanoString nCounter data to housekeeping genes. This is done by subtracting the average log housekeeping gene expression from the expression level of every gene in each sample.

Usage

HKnorm(raw, is.logged = FALSE, corr = 1e-04)

Arguments

raw

data frame of raw counts obtained from nCounter (rows represent genes, columns represent samples). The first three columns must be labeled: c("Code.Class", "Name", "Accession") and contain that information.

is.logged

logical; If TRUE, normalization has already been done on log base 2 scale, no need log the data

corr

small correction to avoid error

Value

data frame of log normalized data in the same format but without reference genes

Author(s)

Aline Talhouk, Derek Chiu

Examples

HKnorm(ovd.r)
HKnorm(ovd.r, is.logged = TRUE)