normalize: Normalization on Affymetrix Probe Level Data or on Expression...
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Warning Author(s) See Also Examples

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

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, ...)

`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.

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.

An object of type DataTreeSet or ExprTreeSet.

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.

Christian Stratowa

express

## 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)