RNAither (version 2.20.0)

quantileNormalization: Quantile normalization

Description

Quantile normalization (see References)

Usage

quantileNormalization(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

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"

References

B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed. A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Variance and Bias. Bioinformatics, 19(2): 185-193, 2003

Examples

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

normres <- quantileNormalization(header, dataset, list(2, "SigIntensity"))
newheader <- normres[[1]]
newdataset <- normres[[2]]