normalizeRatio {cellHTS} | R Documentation |
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.
normalizeRatio(x, fun=function(r1,r2) r2/r1, log=FALSE, scmedian=FALSE, zscore)
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). |
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.
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
.
Ligia Braz ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
..
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)))