Thank you, Sean and all others who replied to me.
   
  First for segmentation method, I am not satisfied with DNAcopy.  A extreme in this case is that when I have a break point near the middle, it could not detect it if I used the SD trim method.  Or it gave too many breaking points.  Also, it can not detect full chromosome change that you have to rely on the ratio.
   
  Is BAC array CGH single strand PCR arrays?  If so, should repeat affact the result?  In my tumor samples with opposite sex for control, I found that the ratio for X varied from sample to sample.  In one sample, it is even 1.  The explaination I got is that chrX has more repeat regions.  Are you suggesting that DNA quality may play a role in this?
   
  I am planning to look at each BAC at one time, comparing tumor vs normal.  Is this a good idea?
   
  Thanks again for your help!
   
  Lisa

Sean Davis <sdavis2@mail.nih.gov> wrote:
  On Thursday 12 October 2006 23:34, Lisa Luo wrote:
> 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?

Lisa,

Segmentation methods (GLAD, DNAcopy, aCGH, etc.) are the way to go here, as 
others have suggested. Averaging is not a good idea given the availability 
of segmentation methods, which accomplish the same goal of reducing noise as 
does averaging, but do so with minimal loss of resolution. 

The ratio is the number of interest, yes. Your normal samples should have a 
ratio of approximately 1, yes. However, because of technical variation, some 
probes and regions may drift a bit away from 1. If you have these 
normal/normal hybs, you can use these to help you to determine where your 
data (in terms of ratio) becomes believable. Another useful measure is to 
look at the ratios that you see on the X-chromosome when comparing two 
samples with different genders in comparison to the ratio that you see for 
the autosomes. 

Finally, were there DNA quality issues that could explain some variation in 
your results? Were the samples amplified or directly labeled?

Sean


 				
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