normalizePlateMedian {cellHTS} | R Documentation |
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.
normalizePlateMedian(x, transform, zscore)
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). |
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.
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
.
Ligia Braz ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
..
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="-")