controlNorm: Normalization on controls

In RNAither: Statistical analysis of high-throughput RNAi screens

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]]

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