tidy_genorm: Calculate reference gene stability

In dhammarstrom/generefer: Functions for finding stable reference genes in qPCR-experiments

Calculate reference gene stability

Description

Calculates M values for n >= 2 genes. When there are more than two genes in the data set, the function calculates M for the full data set, removes the least stable gene (largest M) and calculates M again until only two genes remains. The remaining two genes cannot be ranked. Based on gene ranking normalisation factors (NF) are calculated based on two to n genes and pairwise variations between NFn and NFn+1 are calculated which can be used to determine the optimal number of reference genes to include in the experiment.

Usage

tidy_genorm(dat, sample = "sample", gene = "gene",
  expression = "expression", log = FALSE)

Arguments

dat	Name of the data frame, supplied to the function in i tidy way. A column for sample id ("sample"), a column for gene id ("gene") and a column containing expression values ("expression").
sample	Character column name of column containing sample id's
gene	Character column name of column containing gene id's
expression	Character column name of column containing sample expression values
log	Logical, is data on the log scale?

Value

A list containing: M, a data frame with stability measures, average stability measures per gene after step-wise exclusion of genes; Normalisation factors for n >= 2 genes per sample, and; Pairwise variations of normalisation factors.

References

Vandesompele, J., et al. (2002). "Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes." Genome Biol 3(7)

dhammarstrom/generefer documentation built on April 28, 2024, 6:40 a.m.