normalizeRatio {cellHTS}R Documentation

Normalization of two-color data and data transformation

Description

Normalizes and/or transforms two-channel data xraw of a given 'cellHTS' object by applying the function defined in fun. The default is to take the ratio between the 2 channels (R2/R1). Plate median scaling may also be performed.

Usage

normalizeRatio(x, fun=function(r1,r2) r2/r1, log=FALSE, scmedian=FALSE, zscore)

Arguments

x a cellHTS object that has already been configured (see details).
fun a function defined by the user to relate the signal in the two color channels r1 and r2. fun takes two numeric vectors and returns a numeric vector of the same length. The default is to take the ration between the two channel.
log a logical value indicating whether the result obtained after applying fun should be log2 transformed. The default is log = FALSE, and the data is not log transformed.
scmedian a logical value indicating whether plate median scaling should be performed after applying fun (see details). The default is scmedian = FALSE.
zscore indicates if the z-scores should be determined after normalization and transformation. If missing (default), the data will not be scored. Otherwise, it should be a character string, either "+" or "-", specifying the sign to use for the calculated z-scores (see details).

Details

For each plate and replicate of a two-color experiment, the function defined in fun is applied to relate the intensity values in the two channels of the cellHTS object. The default is to calculate the ration between the second and the first channels, but other options can be defined.

If log = TRUE, the data obtained after applying fun is log2 transformed. The default is log = FALSE.

If scmedian = TRUE, plate median scaling will be further performed, by dividing each measurement by the median value across the wells annotated as sample in the respective plate and replicate. Note that if the data have been log transformed (log = TRUE), the median is subtracted instead. The default is scmedian = FALSE.

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. The overall median and mad 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, except in the dimension corresponding to the number of channels, since the two-channel intensities have been combined into one intensity value.
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("TwoColorScreen", package = "cellHTS")
x = readPlateData("Platelist.txt", "TwoColorData", path=datadir)
confFile = system.file("TwoColorScreen", "Plateconf.txt", package="cellHTS")
logFile  = system.file("TwoColorScreen", "Screenlog.txt", package="cellHTS")
descripFile  = system.file("TwoColorScreen", "Description.txt", package="cellHTS")
x = configure(x, confFile, logFile, descripFile)
#writeReport(x)
x = normalizeRatio(x, fun=function(x,y) x/y, log=TRUE, scmedian=TRUE)
#writeReport(x, force=TRUE, plotPlateArgs=list(xrange=c(-3,3)))

[Package cellHTS version 1.2.0 Index]