[BioC] create CNA object in DNAcopy package with agilent data

[jhs1jjm at leeds.ac.uk]

Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64.

I'm struggling as to what to use for the chromosome and maploc arguments for the
CNA function. I've got data from 3 agilent 44k CGH arrays. I've created the
marrayNorm and Raw objects using read.Agilent. The CNA function usage is as
follows:

CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
                 sampleid=NULL)

I've read the CNA help page but am still struggling.
For genomdat I've worked out this is mnorm at maM, the average log ratios, this
will be my data.type.

The column headers in my raw data file include systematic name in the following
format:

chr3:175483690-175483749

This seems to have been read into my work session using read.Agilent but how do
use this and it isn't ordered, is this important? I've looked at the coriell
data example but this is all nicely ordered and the headers are different to my
data file.

If anyone could point me in the right direction that would be great.

John