normalize {xps}R Documentation

Normalization on Affymetrix Probe Level Data or on Expression Levels

Description

Functions that allow to normalize Affymetrix arrays both at the probe level (“low-level normalization”) and/or at the expression level (“high-level normalization”).

Usage

normalize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "all", method = "mean", option = "transcript:all", logbase = "0", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.02, 0), add.data = TRUE, verbose = TRUE)

normalize.constant(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, method = "mean", logbase = "0", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.02, 0), add.data = TRUE, verbose = TRUE)

normalize.lowess(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, logbase = "log2", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.67, 3), add.data = TRUE, verbose = TRUE)

normalize.quantiles(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", add.data = TRUE, verbose = TRUE)

normalize.supsmu(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, logbase = "log2", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.67, 3), add.data = TRUE, verbose = TRUE)

xpsNormalize(object, ...)

Arguments

xps.data object of class DataTreeSet or ExprTreeSet.
filename file name of ROOT data file.
filedir system directory where ROOT data file should be stored.
tmpdir optional temporary directory where temporary ROOT files should be stored.
update logical. If TRUE the existing ROOT data file filename will be updated.
select type of probes to select for normalization.
method normalization method to use.
option option determining the grouping of probes for normalization, and the selection of the probes.
logbase logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’.
exonlevel exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
refindex index of reference tree to use, or 0.
refmethod for refindex=0, either trimmed mean or median of trees.
params vector of parameters for normalization method.
add.data logical. If TRUE expression data will be included as slot data.
verbose logical, if TRUE print status information.
object object of class DataTreeSet or ExprTreeSet.
... the arguments described above.

Details

Functions that allow to normalize Affymetrix arrays both at the probe level (“low-level normalization”) and/or at the expression level (“high-level normalization”).

xpsNormalize are the DataTreeSet or ExprTreeSet methods, respectively, called by function normalize, containing the same parameters.

Value

An object of type DataTreeSet or ExprTreeSet.

Warning

Functions normalize.lowess and normalize.supsmu have only be tested for objects of type ExprTreeSet but not for objects of type DataTreeSet, i.e. for probe level intensities.

Author(s)

Christian Stratowa

See Also

express

Examples

## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## RMA background
data.bg.rma <- bgcorrect.rma(data.test3,"tmp_Test3NormRMA",filedir=getwd(),tmpdir="",verbose=FALSE)
## normalize quantiles
data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3NormRMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)
## summarize medianpolish
data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3NormRMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)

[Package xps version 1.2.10 Index]