[BioC] Normalization of 2 color Nimblegen array

[Sean Davis]

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