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]