xps (version 1.32.0)

trma: transposed Robust Multi-Array Average Expression Measure

Description

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

Usage

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)

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.

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.

Value

An ExprTreeSet

Details

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

References

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

See Also

rma, xpsRMA, 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="/"))

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()