setupGADAaffy: Imports Affymetrix array data to gada
In gada: Genome Alteration Detection Algorithm (GADA)

Description Usage Arguments Details Value References See Also Examples

This function encapsulates information obtained from Affymetrix platform (APT or Affymetrix Genotyping Console formats) to be analyzed with gada

1	setupGADAaffy(file, NumCols, log2ratioCol, MarkerIdCol = 1, ChrNameCol = 2, ChrPosCol = 3, XY=TRUE, sort = FALSE, orderProbes, saveGenInfo = TRUE)

`file`	A file with Illumina data (obtained from APT or Affymetrix Genotyping Console)
`NumCols`	The number of columns in 'file'
`log2ratioCol`	The column in 'file' containing log2ratio intensities
`MarkerIdCol`	The column in 'file' containing the name of the marker
`ChrNameCol`	The column in 'file' containing the chromosome
`ChrPosCol`	The column in 'file' containing the genomic position
`XY`	Do data have X and Y labels in annotation or 23 and 24? The default is TRUE
`sort`	Should data be sorted using annotation data? The default is TRUE
`orderProbes`	Used when sort is TRUE. See details
`saveGenInfo`	Should annotation data be saved? The default is TRUE. See details

The argument 'saveGenInfo' should not be changed by the user.

An object of class 'setupGADA'

Pique-Regi R, Caceres A, Gonzalez JR. "R-Gada: a package for fast detection and visualization of copy number alterations on multiple samples", BMC Bioinformatics , Submitted Nov 2009

setupGADAIllumina, setupGADAgeneral, setupParGADAaffy

## Not run: 
# get data
download.file("http://www.creal.cat/jrgonzalez/GADA/NA12248_GW6_C.MyTest.CN5.CNCHP.txt",
                 "./NA12248_GW6_C.MyTest.CN5.CNCHP.txt")

dataAffy <- setupGADAaffy(file="NA12248_GW6_C.MyTest.CN5.CNCHP.txt",
                            NumCols=8,log2ratioCol=5)
dataAffy

## End(Not run)