normalizer {chipPCR}

Normalize data

Description

normalizer normalizes any data set using a chosen method (see Details). It may be used when the data from an experiment have considerable variation regarding the background and plateau signal.

Usage

normalizer(y, method.norm = "none", qnL = 0.03)

Arguments

y

is a vector containing the fluorescence values.

method.norm

is a argument to use a "none", "minm", "max", "luqn", or "zscore" normalization. See Details.

qnL

is the quantile to be used for the quantile normalization. Ignored if method.norm is not equal to "luqn".

Details

The parameter qnL is a user defined quantile which is used for the quantile normalization. A quantile normalization herein refers to an approach which is less prone to outliers than a normalization based on the minimum and the maximum of an amplification curve. minm does a min-max normalization between 0 and 1 (see Roediger et al. 2013 for explanation). max does a normalization to the maximum value (MFI/max(MFI)). luqn does a quantile normalization based on a symmetric proportion as defined by the qnL parameter (e.g., qnL = 0.03 equals 3 and 97 percent quantiles). zscore performs a z-score normalization with a mean of 0 and a standard deviation of 1.

Value

A vector of normalized fluorescence values.

Author(s)

Stefan Roediger, Michal Burdukiewicz

References

Surface Melting Curve Analysis with R. S. Roediger, A. Boehm and I. Schimke. The R Journal. 5(2):37–52, 2013. https://journal.r-project.org

See Also

CPP

Examples

normalizer(C17[2L:50, 1], "minm")