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 `object`s 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]