quantileNormalization {RNAither} | R Documentation

## 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]]

[Package RNAither version 2.28.0 Index]