importMAGEML {RMAGEML}R Documentation

import MAGEML documents

Description

This function imports MAGEML documents and creates a marrayRaw object.

Usage

importMAGEML(directory = ".", package = "marray", DED = "none", QTD = "none", name.Rf="none", name.Rb="none", name.Gf="none" ,name.Gb =
"none")

Arguments

directory Directory which contains the MAGEML files that need to be imported
package name of package to which the MAGEML should be imported
DED the DesignElement Dimension
QTD the Quantitation Type 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

getGnames,getArrayLayout, makeMarrayRaw

Examples

data<-system.file("MAGEMLdata", package="RMAGEML")
#will return marrayRaw object.#
importMAGEML(directory = data, package = "marray", 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]