xps (version 1.32.0)

express: Compute expression levels from raw data

Description

This function allows to combine different algorithms to compute expression levels, or to return the result for different algorithms only.

Usage

express(xps.data, filename = character(), filedir = getwd(), tmpdir = "", update = FALSE, # background correction bgcorrect.method = NULL, bgcorrect.select = character(), bgcorrect.option = character(), bgcorrect.params = list(), # normalization normalize.method = NULL, normalize.select = character(), normalize.option = character(), normalize.logbase = character(), normalize.params = list(), # expression values summarize.method = NULL, summarize.select = character(), summarize.option = character(), summarize.logbase = character(), summarize.params = list(), # reference values reference.index  = 0, reference.method = "mean", reference.params = list(0), # misc. exonlevel  = "", xps.scheme = NULL, add.data   = TRUE, bufsize    = 32000, verbose    = TRUE)
xpsPreprocess(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.

bgcorrect.method

background method to use.

bgcorrect.select

type of probes to select for background correction.

bgcorrect.option

type of background correction to use.

bgcorrect.params

vector of parameters for background method.

normalize.method

normalization method to use.

normalize.select

type of probes to select for normalization.

normalize.option

normalization option.

normalize.logbase

logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’.

normalize.params

vector of parameters for normalization method.

summarize.method

summarization method to use.

summarize.select

type of probes to select for summarization.

summarize.option

option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.

summarize.logbase

logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’.

summarize.params

vector of parameters for summarization method.

reference.index

index of reference tree to use, or 0.

reference.method

for refindex=0, either trimmed mean or median of trees.

reference.params

vector of parameters for reference method.

exonlevel

exon annotation level determining which probes should be used for summarization; exon/genome arrays only.

xps.scheme

optional alternative SchemeSet.

add.data

logical. If TRUE expression data will be included as slot data.

bufsize

integer which sets the buffer size of the tree branch baskets (default is 32000).

verbose

logical, if TRUE print status information.

object

object of class DataTreeSet.

...

the arguments described above.

Value

An object of type DataTreeSet or ExprTreeSet.

Details

This function allows to combine different algorithms to compute expression levels, or to return the result for different algorithms only.

Please have a look at vignette “xpsPreprocess.pdf” for details on how to use function express.

xpsPreprocess is the DataTreeSet method called by function express, containing the same parameters.

See Also

bgcorrect, normalize, summarize

Examples

## load existing 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="/"))

## compute rma with a single call to express()
expr.rma <- express(data.test3,"tmp_Test3Exprs",filedir=getwd(),tmpdir="",update=FALSE,
            bgcorrect.method="rma",bgcorrect.select="none",bgcorrect.option="pmonly:epanechnikov",bgcorrect.params=c(16384),
            normalize.method="quantile",normalize.select="pmonly",normalize.option="transcript:together:none",normalize.logbase="0",normalize.params=c(0.0),
            summarize.method="medianpolish",summarize.select="pmonly",summarize.option="transcript",summarize.logbase="log2",summarize.params=c(10, 0.01, 1.0),
            verbose=FALSE)

## get expression data.frame
expr <- exprs(expr.rma)
head(expr)

## plot expression levels
if (interactive()) {
boxplot(expr.rma)
boxplot(log2(expr[,3:6]))
}

## 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="/"))
# 
# workdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Exon/hutissues/exon"
# expr.rma <- express(data.exon,"HuExonExprs",filedir=workdir,tmpdir="",update=F,
#             bgcorrect.method="rma",bgcorrect.select="antigenomic",bgcorrect.option="pmonly:epanechnikov",bgcorrect.params=c(16384),
#             normalize.method="quantile",normalize.select="pmonly",normalize.option="transcript:together:none",normalize.logbase="0",normalize.params=c(0.0),
#             summarize.method="medianpolish",summarize.select="pmonly",summarize.option="transcript",summarize.logbase="log2",summarize.params=c(10, 0.01, 1.0),
#             exonlevel="metacore+affx")
# ## End(Not run)