lowessNorm: Lowess normalization

In RNAither: Statistical analysis of high-throughput RNAi screens

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]]

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.