controlNorm {RNAither} | R Documentation

## 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]]

[Package RNAither version 1.4.2 Index]