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.



On 3/16/06, Khan, Sohail <khan@cshl.edu> wrote:
>
> Dear list,
>
> I have a two color Niblegen array which has a slight spatial effect
> (higher Cy5 in upper left corner).  I have applied loess normalization, but
> it doesn't correct this 'bias".  I can't really apply printtiploess.  Could
> VSN or quantile normaliztion be applied here or could suggest a method to
> normalize this data?
> Thanks.
>
> -Sohail
>
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
>



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Gustavo Henrique Esteves

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Home Page: http://www.vision.ime.usp.br/~gesteves/

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