summarize {xps} | R Documentation

## Probe Set Summarizing Functions

### Description

Converts Affymetrix probe level data to expression levels by summarizing the probe set values into one expression measure and a standard error for this summary.

### Usage

    summarize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(), option = "transcript", logbase = "0", exonlevel = "", params = list(), xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

    summarize.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

    summarize.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

    summarize.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

    xpsSummarize(object, ...)

### Arguments

`xps.data` | object of class `DataTreeSet`.
`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 summarization.
`method` | summarization method to use.
`option` | option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
`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.
`params` | vector of parameters for summarization method.
`xps.scheme` | optional alternative `SchemeTreeSet`.
`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`.
`...` | the arguments described above.

### Details

Converts Affymetrix probe level data to expression levels by summarizing the probe set values into one expression measure and a standard error for this summary.

`xpsSummarize` is the `DataTreeSet` method called by function `summarize`, containing the same parameters.

### Value

An `ExprTreeSet`.

### 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_Test3RMA",filedir=getwd(),tmpdir="",verbose=FALSE)
    ## normalize quantiles
    data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)
    ## summarize medianpolish
    data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)

    ## get expression data.frame
    expr.rma <- exprs(data.mp.rma)
    head(expr.rma)

    ## plot expression levels
    if (interactive()) {
    boxplot(data.mp.rma)
    boxplot(log2(expr.rma[,3:6]))
    }

[Package xps version 1.2.10 Index]