summarize: 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.

Value

An ExprTreeSet.

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.

Examples

Run this code

## 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]))
}