RNAither (version 2.20.0)

ZScorePerScreen: ZScore normalization per experiment

Description

ZScore normalization not per plate, but per experiment (see Value and References)

Usage

ZScorePerScreen(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

- a flag specifying whether controls should be excluded for the computation of the median and median absolute deviation (1) or not (0).

Value

The ZScore is defined as the quotient of the difference between an intensity value and the median of the experiment, and of the median absolute deviation.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"

References

N. Malo et al. Statistical practice in high-throughput screening data analysis. Nature Biotech, 24(2): 167-175, 2006.

See Also

ZScore, BScore

Examples

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

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