lowessNorm {RNAither} | R Documentation

## Lowess normalization

### Description

Performs a plate-wise lowess normalization of the data.

### Usage

    lowessNorm(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 used as channel 1 (colname4ch1) - a character string specifying the column used as channel 2 (colname4ch2) - optionally: the smoother span (smSpan) of the lowess function. This gives the proportion of points which influence the smooth at each value. Larger values give more smoothness. Defaults to 2/3.

### Value

Corrects intensity values in case the values of ch2 decrease with the increase of ch1 values.
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 <- lowessNorm(header, dataset, list("NbCells","SigIntensity"))
    newheader <- normres[[1]]
    newdataset <- normres[[2]]

[Package RNAither version 1.4.2 Index]