bgcorrect: Background Correction

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.

Value

An DataTreeSet

Details

Background corrects probe intensities in an object of class DataTreeSet.

xpsBgCorrect is the DataSet method called by function bgcorrect, 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="/"))

## 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)