Sean Davis | 1 Sep 13:30 2006
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Re: Nimblegen data: oligo, affy, limma?

On Friday 01 September 2006 06:47, J.delasHeras@... wrote:
> I have been using limma for a little while, for the analysis of
> 2-colour cDNA arrays.
>
> I am going to get pretty soon some data from Nimblegen. This will be on
> their promoter arrays, hybridised with some ChIP samples. I understand
> it follows a similar format to Affymetrix, but they use 2-colour hybs.
>
> I'm wondering as to the best way to analyse these. I checked the BioC
> archive for "nimblegen" and I got a couple of things to consider, but I
> am still not sure.
>
> Initially I thought that 'affy' would be the way to go, but since it's
> a 2-colour hyb, I suppose that 'limma' could handle it. In fact, from
> limma I could choose to treat the data as single channel arrays if I
> had to, and I am already familiar with limma. The things I have to
> consider is what method to normalise the data. I read that Loess might
> not be such a good idea for this type of data (ChIP on promoter
> arrays), and perhaps Aquantile would be best. I don't know. I'll have
> to check further. Any pointers greatly appreciated.
>
> Then I found that there's a package somewhere (didn't see it in BioC)
> called 'oligo' that seems to support Nimblegen data, so I would like to
> look into that too. Again, any comments as to how useful this is,
> especially in comparison with limma, would be great.

Nimblegen arrays are actually more similar to two-color arrays, in many 
respects (at least for the chip-chip application).  The manufacturing process 
is similar to Affy (light-directed synthesis), but for the chip-chip 
application, you can think of them as two-color arrays.  The file formats for 
(Continue reading)

J.delasHeras | 1 Sep 14:32 2006
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Re: Nimblegen data: oligo, affy, limma?

Quoting Sean Davis <sdavis2@...>:

> On Friday 01 September 2006 06:47, J.delasHeras@... wrote:
>> I have been using limma for a little while, for the analysis of
>> 2-colour cDNA arrays.
>>
>> I am going to get pretty soon some data from Nimblegen. This will be on
>> their promoter arrays, hybridised with some ChIP samples. I understand
>> it follows a similar format to Affymetrix, but they use 2-colour hybs.
>>
>> I'm wondering as to the best way to analyse these. I checked the BioC
>> archive for "nimblegen" and I got a couple of things to consider, but I
>> am still not sure.
>>
>> Initially I thought that 'affy' would be the way to go, but since it's
>> a 2-colour hyb, I suppose that 'limma' could handle it. In fact, from
>> limma I could choose to treat the data as single channel arrays if I
>> had to, and I am already familiar with limma. The things I have to
>> consider is what method to normalise the data. I read that Loess might
>> not be such a good idea for this type of data (ChIP on promoter
>> arrays), and perhaps Aquantile would be best. I don't know. I'll have
>> to check further. Any pointers greatly appreciated.
>>
>> Then I found that there's a package somewhere (didn't see it in BioC)
>> called 'oligo' that seems to support Nimblegen data, so I would like to
>> look into that too. Again, any comments as to how useful this is,
>> especially in comparison with limma, would be great.
>
> Nimblegen arrays are actually more similar to two-color arrays, in many
> respects (at least for the chip-chip application).  The manufacturing process
(Continue reading)


Gmane