readMageRaw {MAGEML}R Documentation

Creation of marrayRaw object

Description

This function creates a marrayRaw object by using the maLayout and maInfo available from readMageDesign and the raw data file.

Usage

readMageRaw(fname, datadir = ".", name.Gf = "", name.Gb ="", name.Rf =
"", name.Rb="", name.W=NULL, layout = NULL, gnames = NULL, notes=NULL, skip=0, sep="\t",quote="",...)

Arguments

fname File name of file which contains the BioAssayData package
datadir Directory where the files reside
name.Gf Name of green foreground channel
name.Gb Name of green background channel
name.Rf Name of red foreground channel
name.Rb Name of red background channel
name.W Name of weights
notes object of class character, vector of explanatory text
layout The name of the marnotes=NULLrayLayout object that describes the layout of your experiment (made with readMageDesign).
gnames The name of the marrayInfo object that describes the genes of your experiment (made with readMageDesign).
... Further arguments for the `scan' function
skip Further arguments for the `scan' function
quote Further arguments for the `scan' function
sep Further arguments for the `scan' function

Author(s)

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

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

showQuantitationTypes,readMageDesign

Examples

data<-system.file("data", package="MAGEML")
#To obtain list of available quantitation types.#
showQuantitationTypes("Iron.xml",datadir=data)
readMageRaw(fname="Iron.xml",datadir=data,name.Gf="ch1vol",name.Rf="ch2vol",name.Rb="ch2bgmedian",name.Gb="ch1bgmedian")
if(interactive()){
widget.readMageRaw()
}

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