Dear List,

I have a set of BAC array CGH data to analysis.  I am new to this kind of analysis.  Could anyone please recommend me a good package?

I read some papers on aCGH.  For the size of BAC clones, is averaging a few probes a good idea?  I tried DNAcopy and I am not happy with the results either.  Another question:  Can we use the ratio to call it amplification or deletion?  In my normal samples, I should expect ratio to be about 1.  But ratios in some probes/chromosomes tend to be high and ratios in another probes/regions tend to be lower.  So how to use the ratio?

Thank you so much for your help!

Lisa

 		
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