normalize.Probes {Starr} | R Documentation |
Normalization of probe intensities with a given method.
normalize.Probes(eSet, method=NULL, ratio=FALSE, ip, control, description, fkt=median, featureData=FALSE, targets=NULL, arrays = NULL, ...)
eSet |
An ExpressionSet, containing the logged raw intensities |
method |
character string specifying the normalization method to be used. Choices are "none", "scale", "quantile", "Aquantile", "Gquantile", "Rquantile", "Tquantile", "vsn", "rankpercentile", "loess", "substract". |
ratio |
if TRUE, the ratios are calcualted. |
ip |
a boolean vector, indicating which sample are IP experiments |
control |
a boolean vector, indicating which sample are CONTROL experiments |
description |
description of the normalized data |
fkt |
function to chose for averaging over replicates |
featureData |
should the featureData of eSet be passed to the new ExpressionSet? |
targets |
vector, factor or matrix of length twice the number of arrays, used to indicate target groups if method="Tquantile" |
arrays |
Subset of experiments (colnames in ExpressionSet) in the ExpressionSet, that are supposed to be normalized seperately. |
... |
arguments, that should be passed to the normalization methods. |
The procedure calls different functions from this package or from affy and limma, depending on the method.
Calls normalizeWithinArrays
with method="none"
from package limma.
Calls normalizeWithinArrays
with
method="scale"
from package limma.
Calls normalizeBetweenArrays
with
method="quantile"
from package limma.
Calls normalizeBetweenArrays
with
method="Gquantile"
from package limma.
Calls normalizeBetweenArrays
with
method="Rquantile"
from package limma.
Calls normalizeBetweenArrays
with
method="Tquantile"
from package limma.
Calls normalizeBetweenArrays
with
method="Rquantile"
from package limma.
Calls normalizeBetweenArrays
with
method="vsn"
from package limma.
Calls normalize.loess
from package affy.
Calls rankPercentile.normalize
from this package.
Calls substract
from this package.
Benedikt Zacher zacher@lmb.uni-muenchen.de
normalizeBetweenArrays
, normalize.loess
, substract
, rankPercentile.normalize
## # dataPath <- system.file("extdata", package="Starr") # bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) # cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), # file.path(dataPath,"Rpb3_IP2_chr1.cel")) # names <- c("rpb3_1", "wt_1","rpb3_2") # type <- c("IP", "CONTROL", "IP") # rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE) # rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")