varAdjust: Variance adjustment

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Divides the intensity values by their median absolute deviation (of the experiment or of the plate)

Usage

varAdjust(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 screen, 2 a normalization per plate - a flag specifying whether controls should be excluded for the computation of the median absolute deviation (1) or not (0).

Value

Divides the intensity values by their median absolute deviation (of the experiment or of the plate).

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 of the dataset with the suffix ".old"

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

normres <- varAdjust(header, dataset, list(1, "SigIntensity", 1))
newheader <- normres[[1]]
newdataset <- normres[[2]]

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