Variance adjustment

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Description

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

Usage

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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

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

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

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