[BioC] how to analyse single chromosome array CGH data using HMM in aCGH library?

[Ruppert Valentino]

Hello,

I am trying to analyse data from a single chromosome e.g. chromosome 3 
obtained from array CGH using the aCGH library within bioconductor, however 
I get the following error message :

>hmm(ex.acgh)<-find.hmm.states(ex.acgh, delta=1.5)
sample is  1    Chromosomes: 1  Error in kmeans(y, 2) : subscript out of 
bounds
Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x),  :
        attempt to set an attribute on NULL


On troubleshooting this I noticed that the function hmm.run.func() seem to 
analyse data from chromosome 1 to 22.

So question is :

has anyone managed to analyse single chromosome data using aCGH and if so I 
would be grateful if I can have a look at the modified hmm.run.func() 
function that they wrote, otherwise can anyone suggest alternative software 
that one can use to analyse data from single chromosome. This will be of 
interest to researchers who carry out titling path arrays after doing the 
1MB aarray CGH for example.


Many thanks.

Ruppert

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