summarize: Probe Set Summarizing Functions

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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]))
}

xps documentation built on Nov. 8, 2020, 6 p.m.