[BioC] Normalization of 2 color Nimblegen array

[Rafael A. Irizarry]

Hi! I just wanted to point out that the oligo package supports nimblegen
arrays (you need the xys and ndf) files. It is under development but we 
need testers. If anybody wants a specific method or function 
incorporated you can email benitlon or me. Most functions in the affy 
package can be easily exproted.

-r

On Thu, 16 Mar 2006, Sean Davis wrote:

>
>
>
> On 3/16/06 9:36 AM, "Gustavo H. Esteves" <gesteves at gmail.com> wrote:
>
>> Dear Khan,
>>
>> do you know package OLIN from Bioconductor? Have a look at this package.
>>
>> It does the loess normalization with a step of estimation of the best span
>> parameters and then does another loess regression for the x and y location
>> in the chip.
>>
>> The main reference for this normalization method is:
>> Futschik, M. & Crompton, T. Model selection and efficiency testing for
>> normalization of cDNA microarray data Genome Biology, 2004, 5, R60
>>
>> Good Luck.
>
> Thanks, Gustavo, for the pointer--I learned something!
>
> Just to be a bit more explicit on my earlier email, keep in mind here that
> loess normalization on an M vs. A plot (MA plot) assumes that there is no
> intensity-dependent signal (ie., that the log-ratios should be centered
> around 0).  In fact, for many nimblegen applications, there IS
> intensity-dependent signal (ie., one expects higher-intensity spots to have
> a higher log ratio).  In fact, for the "best" arrays, one would expect an MA
> plot to have a positive slope if fit with a regression line.  Therefore, if
> one uses loess normalization (in the MA plot sense), one is definitely
> normalizing out the signal!  For expression arrays, the usual assumptions
> apply and this isn't an issue--loess away!  That is why it is important to
> know the application before choosing a normalization method.
>
> Sean
>
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