express: Compute expression levels from raw data
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Author(s) See Also Examples

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

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, ...)

`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.

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.

An object of type DataTreeSet or ExprTreeSet.

Christian Stratowa

bgcorrect, normalize, summarize

## 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)