bgcorrect: Background Correction

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

Description

Background corrects probe intensities in an object of class DataTreeSet.

Usage

bgcorrect(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(0), option = character(0), exonlevel = "", params = list(), verbose = TRUE)

bgcorrect.gc(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "antigenomic", exonlevel = "", verbose = TRUE)

bgcorrect.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "all", exonlevel = "", verbose = TRUE)

bgcorrect.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "both", exonlevel = "", verbose = TRUE)

bgcorrect.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", exonlevel = "", verbose = TRUE)

xpsBgCorrect(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 background correction.
method	background method to use.
option	type of background correction to use.
exonlevel	exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
params	vector of parameters for background method.
verbose	logical, if TRUE print status information.
object	object of class DataSet.
...	the arguments described above.

Details

Background corrects probe intensities in an object of class DataTreeSet.

xpsBgCorrect is the DataSet method called by function bgcorrect, containing the same parameters.

Value

An DataTreeSet

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="/"))

## MAS4 sector background
data.bg.mas4 <- bgcorrect.mas4(data.test3,"tmp_Test3MAS4Bgrd",filedir=getwd(),tmpdir="",verbose=FALSE)

## need to attach background intensities
data.bg.mas4 <- attachBgrd(data.bg.mas4)

## get data.frame
bg.mas4 <- validBgrd(data.bg.mas4)
head(bg.mas4)

## plot images
if (interactive()) {
image.dev(data.bg.mas4,bg=TRUE,col=rainbow(32))
image(matrix(bg.mas4[,1], ncol=ncols(schemeSet(data.bg.mas4)), nrow=nrows(schemeSet(data.bg.mas4))))
}

## Not run: 
## examples using Affymetrix human tissue dataset (see also xps/examples/script4exon.R)

## example - exon array, e.g. HuEx-1_0-st-v2:
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData"
scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/"))
data.exon   <- root.data(scheme.exon, paste(datdir,"HuTissuesExon_cel.root",sep="/"))

## compute rma background
workdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Exon/hutissues/exon"
data.bg.rma <- bgcorrect(data.exon, "HuExonRMABgrd", filedir=workdir, tmpdir="", 
               method="rma", select="antigenomic", option="pmonly:epanechnikov",
               params=c(16384), exonlevel="metacore+affx")

# or alternatively:
data.bg.rma <- bgcorrect.rma(data.exon, "HuExonRMABgrd", filedir=workdir, tmpdir="", 
               select="antigenomic", exonlevel="metacore+affx")

## End(Not run)

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