RNAither (version 2.20.0)

controlNorm: Normalization on controls

Description

Performs a normalization on either positive or negative controls.

Usage

controlNorm(header, dataset, listOfArgs)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

listOfArgs

a list containing: - a character string specifying the column whose values will be used for normalization - 1 or 2, 1 meaning a normalization per experiment, 2 meaning a normalization per plate - 0 or 1, 0 meaning a normalization on the median of negative controls, 1 meaning a normalization on the median of positive controls. Can also be the GeneName of a specific control siRNA - 1 or 2, 1 meaning the signal values are divided by the median, 2 meaning the median is subtracted from the signal values

Value

Returns a list containing:

header

the new header (with an added entry about the normalization procedure in the comments).

dataset

the new dataset with normalized values. The old values are saved in an extra column with the suffix ".old".

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

normres <- controlNorm(header, dataset, list(2, 0, "SigIntensity", 1))

newheader <- normres[[1]]
newdataset <- normres[[2]]