normalizePlateMedian {cellHTS}R Documentation

Median normalization of the data and data transformation

Description

Plate median normalization of the data xraw of a cellHTS object. Optionally, a data transformation such log, and a transformation to z-scores can be performed.

Usage

normalizePlateMedian(x, transform, zscore)

Arguments

x a cellHTS object that has already been configured (see details).
transform a function that takes a numeric vector and returns a numeric vector of the same length; for example, the logarithm function log.
zscore indicates if the data should be centered and scaled after normalization and transformation. If missing (default), the data will not be centered and scaled. Otherwise, the value of this argument should be a character string, either "+" or "-", which will be used to set the sign for the calculated z-scores (see details).

Details

For each plate, replicate and batch, the median value across the wells annotated as sample in x$wellAnno is calculated. Then, every measurement is divided by this value.

If transform is not missing, the chosen data transformation is applied. Most commonly, this option can be used to apply a log transformation.

If zscore is not missing, a robust z-score for each individual measurement will be determined for each plate and each well by subtracting the overall median and dividing by the overall mad. These are taken by considering the distribution of intensities (over all plates) in the wells whose content is annotated as sample. The allowed values for zscore ("+" or "-") are used to set the sign of the calculated z-scores. For example, with a zscore="-" a strong decrease in the signal will be represented by a positive z-score, whereas setting zscore="+", such a phenotype will be represented by a negative z-score. This option can be set to calculate the results to the commonly used convention.

Value

An object of class cellHTS, which is a copy of the argument x, plus an additional slot xnorm containing the normalized data. This is an array of the same dimensions as xraw.
Moreover, the processing status of the cellHTS object is updated in the slot state to state["normalized"]=TRUE.

Author(s)

Ligia Braz ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

References

..

Examples

 datadir = system.file("KcViabSmall", package = "cellHTS")
 x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
 confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
 logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
 descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
 x = configure(x, confFile, logFile, descripFile)
 x = normalizePlateMedian(x, zscore="-")

[Package cellHTS version 1.2.0 Index]