RNAither (version 2.20.0)

divNorm: Mean, median, ... , normalization

Description

Normalization with the mean, median, or any other function.

Usage

divNorm(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

- a function to be used for the normalization, e.g. mean, median, ...

- 1 or 2, 1 meaning a normalization per experiment, 2 meaning a normalization per plate

- 1 or 2, 1 meaning the normalization is achieved by a division of the intensity values by the outcome of funname, 2, meaning by a substraction

- a flag specifying whether controls should be excluded for the computation of the result of the function specified in the first element (1) or not (0).

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 <- divNorm(header, dataset, list(median, 2, 1, "SigIntensity", 1))

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