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

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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, 0.0, 0.0), 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(0.0, 0.0, 0.0, 0.0), 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”).

Please have a look at vignette “xpsPreprocess.pdf” for details on how to use function normalize.

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

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## 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)

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