trma: transposed Robust Multi-Array Average Expression Measure
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) References See Also Examples

This function converts a DataTreeSet into an ExprTreeSet using the transposed robust multi-array average (RMA) expression measure.

trma(xps.data,
     filename   = character(0),
     filedir    = getwd(),
     tmpdir     = "",
     background = "pmonly",
     normalize  = TRUE,
     option     = "transcript",
     exonlevel  = "",
     params     = list(16384, 0.0, 1.0, 10, 0.01, 2),
     xps.scheme = NULL,
     add.data   = TRUE,
     verbose    = TRUE)

`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.
`background`	probes used to compute background, one of ‘pmonly’, ‘mmonly’, ‘both’; for genome/exon arrays one of ‘genomic’, ‘antigenomic’
`normalize`	logical. If `TRUE` normalize data using quantile normalization.
`option`	option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
`exonlevel`	exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
`params`	list of (default) parameters for `rma`.
`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.

This function computes the tRMA (transposed Robust Multichip Average) expression measure described in Giorgi et al. for both expression arrays and exon arrays.

To use method xpsRMA or function express to compute trma you need to set params = list(16384, 0.0, 1.0, 10, 0.01, 2).

For further details please see rma

An ExprTreeSet

Christian Stratowa

Federico M. Giorgi, Anthony M. Bolger, Marc Lohse and Bjoern Usadel (2010), Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinformatics 11:553

rma, xpsRMA, express

## 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="/"))

data.trma <- trma(data.test3,"tmp_Test3tRMA",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)

## get data.frame
expr.trma <- validData(data.trma)
head(expr.trma)

rm(scheme.test3, data.test3)
gc()