Single channel CGH analysis [was Re: Bioconductor Digest, Vol 62, Issue 3]
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@sean-davis-490
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On Fri, Apr 4, 2008 at 1:56 PM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > Hi Sean > > Thanks, I am using arrary CGH from Agilent (244K), which is custom designed > using their earray software. In one array slide I have hybridized my test > sample and I would like to compare the same with a reference which i have > hybridized in another slide. > Can you advise on this scenario? > > Abhilash Hi, Abhilash. It is unfortunate that the experiment was performed this way. That said, you can certainly make a ratio of the signal from each of the two arrays and treat it as 2-color CGH. Once you have log ratios, any of the typical CGH analysis packages could be applied. Sean > > On Fri, Apr 4, 2008 at 5:21 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > On Fri, Apr 4, 2008 at 4:03 AM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > > > Hi all, > > > > > > I would like to find out the methods for analysis of single channel > array > > > CGH. Can I perform the same with CGH package? Or is there any better > way to > > > explore the possibility? > > > > Hi, Abhilash. Generally, you will want to start a new message and not > > reply to another message when writing to the list. > > > > As to your question, you will need to be specific about what array > > platform you are using. > > > > Sean > > > > > > -- > > Regards, > Abhilash
CGH CGH • 582 views
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Abhilash Venu ▴ 340
@abhilash-venu-2680
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On Fri, Apr 4, 2008 at 2:42 PM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > Hi Sean, > > Thanks Sean. > One more question. Do you feel that the experimental design is wrong or it > has some major problems? Besides losing the advantage of the two-color system, the experimental costs are approximately double what they could have been if only one slide and two colors were used. Sean > Abhilash > > > > On Fri, Apr 4, 2008 at 11:35 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > > > On Fri, Apr 4, 2008 at 1:56 PM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > > > Hi Sean > > > > > > Thanks, I am using arrary CGH from Agilent (244K), which is custom > designed > > > using their earray software. In one array slide I have hybridized my > test > > > sample and I would like to compare the same with a reference which i > have > > > hybridized in another slide. > > > Can you advise on this scenario? > > > > > > Abhilash > > > > Hi, Abhilash. It is unfortunate that the experiment was performed > > this way. That said, you can certainly make a ratio of the signal > > from each of the two arrays and treat it as 2-color CGH. Once you > > have log ratios, any of the typical CGH analysis packages could be > > applied. > > > > Sean > > > > > > > > > > > > > > > > On Fri, Apr 4, 2008 at 5:21 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > > On Fri, Apr 4, 2008 at 4:03 AM, Abhilash Venu <abhivenu at="" gmail.com=""> > wrote: > > > > > Hi all, > > > > > > > > > > I would like to find out the methods for analysis of single channel > > > array > > > > > CGH. Can I perform the same with CGH package? Or is there any > better > > > way to > > > > > explore the possibility? > > > > > > > > Hi, Abhilash. Generally, you will want to start a new message and not > > > > reply to another message when writing to the list. > > > > > > > > As to your question, you will need to be specific about what array > > > > platform you are using. > > > > > > > > Sean > > > > > > > > > > > > > > > > -- > > > > > > Regards, > > > Abhilash > > > > > > -- > > Regards, > Abhilash
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