makeMarrayRaw {RMAGEML}R Documentation

Creation of a marrayRaw object

Description

This function creates a marrayRaw object.

Usage

makeMarrayRaw(mageOM, layout, gnames, directory = ".", DED = "none", QTD = "none", name.Rf = "none", name.Rb = "none", name.Gf = "none" ,name.Gb = "none")

Arguments

mageOM Reference to MAGE Object Model
directory Directory which contains the MAGEML files that need to be imported
gnames the Gnames marrayInfo object e.g. created by getGnames
layout the marrayLayout object e.g. created by getLayout
QTD the Quantitation Type Dimension
DED the Design Element Dimension
name.Rf the name of the red foreground intensity
name.Rb the name of the red background intensity
name.Gf the name of the green foreground intensity
name.Gb the name of the green background intensity

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
Joke Allemeersch, http://www.esat.kuleuven.ac.be/~jallemee.

References

Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr and Brazma A. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23;3(9):RESEARCH0046.

See Also

importMAGEOM, getGnames, getArrayLayout

Examples

data<-system.file("MAGEMLdata", package="RMAGEML")
#To obtain a marrayInfo object containing the database identifiers of the features present on the array.#
mageom<-importMAGEOM(directory=data)
gnames<-getGnames(mageom, DED = "DED:707")
layout<-getArrayLayout(mageom)
makeMarrayRaw(mageOM=mageom, layout = layout, gnames = gnames, directory = data, DED = "DED:707",QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")

[Package RMAGEML version 2.1.0 Index]