RNAither (version 2.20.0)

lowessNorm: 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]]