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]